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7282 lines
284 KiB
Python
7282 lines
284 KiB
Python
# Copyright 2023 by Michiel de Hoon. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests for Align.chain module."""
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import unittest
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from io import StringIO
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from tempfile import NamedTemporaryFile
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from Bio import Align
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from Bio import SeqIO
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from Bio.Align import Alignment
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from Bio.Seq import reverse_complement
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from Bio.Seq import Seq
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from Bio.SeqFeature import CompoundLocation
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from Bio.SeqFeature import ExactPosition
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from Bio.SeqFeature import SimpleLocation
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from Bio.SeqRecord import SeqRecord
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try:
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import numpy as np
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except ImportError:
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from Bio import MissingPythonDependencyError
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raise MissingPythonDependencyError(
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"Install numpy if you want to use Bio.Align.chain."
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) from None
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class TestAlign_dna_rna(unittest.TestCase):
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# The chain file dna_rna.chain was generated from the PSL file using:
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# pslToChain dna_rna.psl dna_rna.chain
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def setUp(self):
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data = {}
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records = SeqIO.parse("Blat/dna.fa", "fasta")
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for record in records:
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name, start_end = record.id.split(":")
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assert name == "chr3"
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start, end = start_end.split("-")
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start = int(start)
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end = int(end)
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sequence = str(record.seq)
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assert len(sequence) == end - start
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data[start] = sequence
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self.dna = data
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records = SeqIO.parse("Blat/rna.fa", "fasta")
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self.rna = {record.id: record.seq for record in records}
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def check_alignments(self, alignments):
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alignment = next(alignments)
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self.assertEqual(alignment.shape, (2, 1711))
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self.assertEqual(len(alignment), 2)
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self.assertEqual(alignment.score, 176)
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self.assertIs(alignment.sequences[0], alignment.target)
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self.assertIs(alignment.sequences[1], alignment.query)
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self.assertEqual(alignment.target.id, "chr3")
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self.assertEqual(alignment.query.id, "NR_046654.1")
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self.assertEqual(len(alignment.target.seq), 198295559)
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self.assertEqual(len(alignment.query.seq), 181)
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self.assertTrue(
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np.array_equal(
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alignment.coordinates,
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# fmt: off
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np.array([[42530895, 42530958, 42532020, 42532095, 42532563, 42532606],
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[ 181, 118, 118, 43, 43, 0]])
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# fmt: on
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)
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)
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dna = Seq(self.dna, length=len(alignment.target))
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alignment.target.seq = dna
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alignment.query.seq = self.rna[alignment.query.id]
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self.assertTrue(
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np.array_equal(
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alignment.substitutions,
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# fmt: off
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np.array([[36., 0., 0., 0., 0., 0., 0., 0.],
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[ 0., 40., 0., 0., 0., 0., 0., 0.],
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[ 0., 0., 57., 0., 0., 0., 0., 0.],
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[ 0., 0., 0., 42., 0., 0., 0., 0.],
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[ 2., 0., 0., 0., 0., 0., 0., 0.],
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[ 0., 1., 0., 0., 0., 0., 0., 0.],
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[ 0., 0., 3., 0., 0., 0., 0., 0.],
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[ 0., 0., 0., 0., 0., 0., 0., 0.],
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])
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# fmt: on
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)
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)
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self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
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self.assertEqual(
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str(alignment),
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"""\
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chr3 42530895 CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCC
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0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NR_046654 181 CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCC
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chr3 42530955 AGGCTGGGGACAGAGGGGGCAAGGCCTGGAGAACTCCCTAGGGGGAGGGTGCCAACCCAG
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60 |||---------------------------------------------------------
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NR_046654 121 AGG---------------------------------------------------------
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chr3 42531015 CTTGCAGTCCTACGTCTTGCTTAGCTGCAGGTCCTGCCTGCAAGGATATCAGCCAAGGGT
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120 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531075 CAAGAAAGTCCTCAAAATGTCTGATCCCAGGACAAGTCCCTCAGGTTGCAGCTGCACCTA
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180 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531135 GGGCTGACCTGTGGGACAGATTTTGTGAACATCTTTCCATTTCCCTTTAGTTCCCGAAAT
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240 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531195 ACAcagggccactgctaatctataaagggcctctgtcacaattagaaagagaatgtccgt
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300 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531255 ctaggtagacacagcccttcaggcatacagcttCACCCCCTCAGTGGAGCATCCCTCCGT
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360 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531315 GGTGAACAACCTATGCAACCAAAGACAGCAGACTGACAACCCACCCTTTtctctctccct
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420 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531375 ccctctccctgcttttctccaaaatctctccctcatgccctctacccctgcttcctgtgc
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480 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531435 cctctctgctctttcactctccctGGGCCTGACAGGGGTACCCAGCACATTCACCATGGT
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540 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531495 GTGGACCATCGCCAGGATCCATTTTGAGGATTATGGGTGAGCTGCTGCCCCACACACTCC
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600 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531555 CCCGGCCGCCATCACTTGGGCAGGCCCCCTGGGTGGGATGATAATGCCATCTGGCCTTGG
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660 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531615 TGAGTGGACAAAAACCACAGCTCTCGGGCCAGAGGGGAGGCTGGAGGAGGACCTGGGGAG
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720 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531675 CAACAGACTCTGGGCCCGGGGTTGCTAAAGTGCTCAGGAGCAGAGCTGGGGACAACTGGG
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780 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531735 GGAGGTGCTGCTGAGTCTCTCTCTGGCTGAGGACAATCCCTCTCATTCCTCCCCACGGTC
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840 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531795 TGCTCAGGTGCTGGGACACCATCAACTCCTCACTGTGGTGGATCATAAAGGGCCCCATCC
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900 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531855 TCACCTCCATCTTGGTAAGATaccctcccaccacctagagatggggaaacaggcccaaag
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960 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531915 ggcaggcaacttagcccaaggtcacatgggaaattagtatctaggtcagaactgaaacgt
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1020 ------------------------------------------------------------
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NR_046654 118 ------------------------------------------------------------
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chr3 42531975 agcttcctaatgcccaatgcaggatcatccccacccctgtcctaccagTTCTTCCTTGAG
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1080 ---------------------------------------------...||||||||||||
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NR_046654 118 ---------------------------------------------CAGTTCTTCCTTGAG
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chr3 42532035 CGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGAC
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1140 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NR_046654 103 CGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGAC
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chr3 42532095 CTGCCCAAAGGGGAAATGCCAGAGGAGAGGTAAGATAGAGAGAGGGGCAGCAGGACCCTG
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1200 ------------------------------------------------------------
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NR_046654 43 ------------------------------------------------------------
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chr3 42532155 GGAAAGAAGACAGGCCAGCAGTCAAGGGGCCTGAACACCTCAGCCTTCCCGCTCTGACTG
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1260 ------------------------------------------------------------
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NR_046654 43 ------------------------------------------------------------
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chr3 42532215 CCCGAACTCGGGTCCCCACCCACTAGGTAAACTTCATCCTGTTTATTTGCATCATCCGAA
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1320 ------------------------------------------------------------
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NR_046654 43 ------------------------------------------------------------
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chr3 42532275 TCCTGCTTCAGAAACTGCGGCCCCCAGATATCAGGAAGAGTGACAGCAGTCCATACTCGT
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1380 ------------------------------------------------------------
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NR_046654 43 ------------------------------------------------------------
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chr3 42532335 GAGTGTGGGCCTAGTGCCTCAGCCCCCAGTACCTCCATCCCCAGTCCTCAAATCATCCCA
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1440 ------------------------------------------------------------
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NR_046654 43 ------------------------------------------------------------
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chr3 42532395 CATCTCCTTGAAGTCCTCCCACCCCAAACATCCAGAGTCACCAAAGAGCCACATTGTTCT
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1500 ------------------------------------------------------------
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NR_046654 43 ------------------------------------------------------------
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chr3 42532455 TTCCCACCTCCACCATGGCCTGGCTcagcccaccaccatcccctgctccagccccaccct
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1560 ------------------------------------------------------------
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NR_046654 43 ------------------------------------------------------------
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chr3 42532515 caCCAGGCTGCACTCAGAGCCCTGCATGCTTCTCCTGCCCACACTCACCTAGCATCCTTC
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1620 ------------------------------------------------||||||||||||
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NR_046654 43 ------------------------------------------------CTAGCATCCTTC
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chr3 42532575 CCAGGTATGCATCTGCTGCCAAGCCAGGgag 42532606
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1680 ||||||||||||||||||||||||||||... 1711
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NR_046654 31 CCAGGTATGCATCTGCTGCCAAGCCAGGGAG 0
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""",
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)
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self.assertEqual(
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format(alignment, "chain"),
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"""\
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chain 176 chr3 198295559 + 42530895 42532606 NR_046654.1 181 - 0 181 1
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63 1062 0
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75 468 0
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43
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""",
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)
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counts = alignment.counts()
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self.assertEqual(
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repr(counts),
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"<AlignmentCounts object (181 aligned letters; 175 identities; 6 mismatches; 1530 gaps) at 0x%x>"
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% id(counts),
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)
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self.assertEqual(
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str(counts),
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"""\
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AlignmentCounts object with
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aligned = 181:
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identities = 175,
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mismatches = 6.
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gaps = 1530:
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left_gaps = 0:
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left_insertions = 0:
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open_left_insertions = 0,
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extend_left_insertions = 0;
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left_deletions = 0:
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open_left_deletions = 0,
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extend_left_deletions = 0;
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internal_gaps = 1530:
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internal_insertions = 0:
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open_internal_insertions = 0,
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extend_internal_insertions = 0;
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internal_deletions = 1530:
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open_internal_deletions = 2,
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extend_internal_deletions = 1528;
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right_gaps = 0:
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right_insertions = 0:
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open_right_insertions = 0,
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extend_right_insertions = 0;
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right_deletions = 0:
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open_right_deletions = 0,
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extend_right_deletions = 0.
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""",
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)
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self.assertEqual(counts.left_insertions, 0)
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self.assertEqual(counts.left_deletions, 0)
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self.assertEqual(counts.right_insertions, 0)
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self.assertEqual(counts.right_deletions, 0)
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self.assertEqual(counts.internal_insertions, 0)
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self.assertEqual(counts.internal_deletions, 1530)
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self.assertEqual(counts.left_gaps, 0)
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self.assertEqual(counts.right_gaps, 0)
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self.assertEqual(counts.internal_gaps, 1530)
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self.assertEqual(counts.insertions, 0)
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self.assertEqual(counts.deletions, 1530)
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self.assertEqual(counts.gaps, 1530)
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self.assertEqual(counts.aligned, 181)
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self.assertEqual(counts.identities, 175)
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self.assertEqual(counts.mismatches, 6)
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alignment = next(alignments)
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self.assertEqual(alignment.shape, (2, 1714))
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self.assertEqual(len(alignment), 2)
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self.assertIs(alignment.sequences[0], alignment.target)
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self.assertIs(alignment.sequences[1], alignment.query)
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self.assertEqual(alignment.target.id, "chr3")
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self.assertEqual(alignment.query.id, "NR_046654.1_modified")
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self.assertEqual(len(alignment.target.seq), 198295559)
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self.assertEqual(len(alignment.query.seq), 190)
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self.assertTrue(
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np.array_equal(
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alignment.coordinates,
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# fmt: off
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np.array([[42530895, 42530922, 42530922, 42530958, 42532020,
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42532037, 42532039, 42532095, 42532563, 42532606],
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[ 185, 158, 155, 119, 119,
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102, 102, 46, 46, 3],
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])
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# fmt: on
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)
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)
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dna = Seq(self.dna, length=len(alignment.target))
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alignment.target.seq = dna
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alignment.query.seq = self.rna[alignment.query.id]
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self.assertTrue(
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np.array_equal(
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alignment.substitutions,
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# fmt: off
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np.array([[34., 0., 0., 1., 0., 0., 0., 0.],
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[ 0., 40., 0., 0., 0., 0., 0., 0.],
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[ 0., 0., 57., 0., 0., 0., 0., 0.],
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[ 0., 0., 0., 41., 0., 0., 0., 0.],
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[ 2., 0., 0., 0., 0., 0., 0., 0.],
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[ 0., 1., 0., 0., 0., 0., 0., 0.],
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[ 0., 0., 3., 0., 0., 0., 0., 0.],
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[ 0., 0., 0., 0., 0., 0., 0., 0.],
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]),
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# fmt: on
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)
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)
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self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
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self.assertEqual(
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str(alignment),
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"""\
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chr3 42530895 CGGAAGTACTTCTGGGGGTACATACTC---ATCGGCTGGGGTATGGTACCAGGGAGGGCT
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0 |||||||||||||||||||||||||||---||||||||||||||||||||||||||||||
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NR_046654 185 CGGAAGTACTTCTGGGGGTACATACTCCCCATCGGCTGGGGTATGGTACCAGGGAGGGCT
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chr3 42530952 TCCAGGCTGGGGACAGAGGGGGCAAGGCCTGGAGAACTCCCTAGGGGGAGGGTGCCAACC
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60 ||||||------------------------------------------------------
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NR_046654 125 TCCAGG------------------------------------------------------
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chr3 42531012 CAGCTTGCAGTCCTACGTCTTGCTTAGCTGCAGGTCCTGCCTGCAAGGATATCAGCCAAG
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120 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
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chr3 42531072 GGTCAAGAAAGTCCTCAAAATGTCTGATCCCAGGACAAGTCCCTCAGGTTGCAGCTGCAC
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180 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
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chr3 42531132 CTAGGGCTGACCTGTGGGACAGATTTTGTGAACATCTTTCCATTTCCCTTTAGTTCCCGA
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240 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
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chr3 42531192 AATACAcagggccactgctaatctataaagggcctctgtcacaattagaaagagaatgtc
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300 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
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chr3 42531252 cgtctaggtagacacagcccttcaggcatacagcttCACCCCCTCAGTGGAGCATCCCTC
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360 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
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chr3 42531312 CGTGGTGAACAACCTATGCAACCAAAGACAGCAGACTGACAACCCACCCTTTtctctctc
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420 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
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|
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chr3 42531372 cctccctctccctgcttttctccaaaatctctccctcatgccctctacccctgcttcctg
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480 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
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|
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chr3 42531432 tgccctctctgctctttcactctccctGGGCCTGACAGGGGTACCCAGCACATTCACCAT
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540 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
|
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|
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chr3 42531492 GGTGTGGACCATCGCCAGGATCCATTTTGAGGATTATGGGTGAGCTGCTGCCCCACACAC
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600 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
|
|
|
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chr3 42531552 TCCCCCGGCCGCCATCACTTGGGCAGGCCCCCTGGGTGGGATGATAATGCCATCTGGCCT
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660 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
|
|
|
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chr3 42531612 TGGTGAGTGGACAAAAACCACAGCTCTCGGGCCAGAGGGGAGGCTGGAGGAGGACCTGGG
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720 ------------------------------------------------------------
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NR_046654 119 ------------------------------------------------------------
|
|
|
|
chr3 42531672 GAGCAACAGACTCTGGGCCCGGGGTTGCTAAAGTGCTCAGGAGCAGAGCTGGGGACAACT
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780 ------------------------------------------------------------
|
|
NR_046654 119 ------------------------------------------------------------
|
|
|
|
chr3 42531732 GGGGGAGGTGCTGCTGAGTCTCTCTCTGGCTGAGGACAATCCCTCTCATTCCTCCCCACG
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|
840 ------------------------------------------------------------
|
|
NR_046654 119 ------------------------------------------------------------
|
|
|
|
chr3 42531792 GTCTGCTCAGGTGCTGGGACACCATCAACTCCTCACTGTGGTGGATCATAAAGGGCCCCA
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|
900 ------------------------------------------------------------
|
|
NR_046654 119 ------------------------------------------------------------
|
|
|
|
chr3 42531852 TCCTCACCTCCATCTTGGTAAGATaccctcccaccacctagagatggggaaacaggccca
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|
960 ------------------------------------------------------------
|
|
NR_046654 119 ------------------------------------------------------------
|
|
|
|
chr3 42531912 aagggcaggcaacttagcccaaggtcacatgggaaattagtatctaggtcagaactgaaa
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|
1020 ------------------------------------------------------------
|
|
NR_046654 119 ------------------------------------------------------------
|
|
|
|
chr3 42531972 cgtagcttcctaatgcccaatgcaggatcatccccacccctgtcctaccagTTCTTCCTT
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1080 ------------------------------------------------...|||||||||
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NR_046654 119 ------------------------------------------------CAGTTCTTCCTT
|
|
|
|
chr3 42532032 GAGCGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGAT
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1140 |||||--|||||||||||.|||||||||||||||||||||||||||||||||||||||||
|
|
NR_046654 107 GAGCG--AGCGGATTGGGTGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGAT
|
|
|
|
chr3 42532092 GACCTGCCCAAAGGGGAAATGCCAGAGGAGAGGTAAGATAGAGAGAGGGGCAGCAGGACC
|
|
1200 |||---------------------------------------------------------
|
|
NR_046654 49 GAC---------------------------------------------------------
|
|
|
|
chr3 42532152 CTGGGAAAGAAGACAGGCCAGCAGTCAAGGGGCCTGAACACCTCAGCCTTCCCGCTCTGA
|
|
1260 ------------------------------------------------------------
|
|
NR_046654 46 ------------------------------------------------------------
|
|
|
|
chr3 42532212 CTGCCCGAACTCGGGTCCCCACCCACTAGGTAAACTTCATCCTGTTTATTTGCATCATCC
|
|
1320 ------------------------------------------------------------
|
|
NR_046654 46 ------------------------------------------------------------
|
|
|
|
chr3 42532272 GAATCCTGCTTCAGAAACTGCGGCCCCCAGATATCAGGAAGAGTGACAGCAGTCCATACT
|
|
1380 ------------------------------------------------------------
|
|
NR_046654 46 ------------------------------------------------------------
|
|
|
|
chr3 42532332 CGTGAGTGTGGGCCTAGTGCCTCAGCCCCCAGTACCTCCATCCCCAGTCCTCAAATCATC
|
|
1440 ------------------------------------------------------------
|
|
NR_046654 46 ------------------------------------------------------------
|
|
|
|
chr3 42532392 CCACATCTCCTTGAAGTCCTCCCACCCCAAACATCCAGAGTCACCAAAGAGCCACATTGT
|
|
1500 ------------------------------------------------------------
|
|
NR_046654 46 ------------------------------------------------------------
|
|
|
|
chr3 42532452 TCTTTCCCACCTCCACCATGGCCTGGCTcagcccaccaccatcccctgctccagccccac
|
|
1560 ------------------------------------------------------------
|
|
NR_046654 46 ------------------------------------------------------------
|
|
|
|
chr3 42532512 cctcaCCAGGCTGCACTCAGAGCCCTGCATGCTTCTCCTGCCCACACTCACCTAGCATCC
|
|
1620 ---------------------------------------------------|||||||||
|
|
NR_046654 46 ---------------------------------------------------CTAGCATCC
|
|
|
|
chr3 42532572 TTCCCAGGTATGCATCTGCTGCCAAGCCAGGgag 42532606
|
|
1680 |||||||||||||||||||||||||||||||... 1714
|
|
NR_046654 37 TTCCCAGGTATGCATCTGCTGCCAAGCCAGGGAG 3
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 170 chr3 198295559 + 42530895 42532606 NR_046654.1_modified 190 - 5 187 2
|
|
27 0 3
|
|
36 1062 0
|
|
17 2 0
|
|
56 468 0
|
|
43
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (179 aligned letters; 172 identities; 7 mismatches; 1535 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 179:
|
|
identities = 172,
|
|
mismatches = 7.
|
|
gaps = 1535:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 1535:
|
|
internal_insertions = 3:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 2;
|
|
internal_deletions = 1532:
|
|
open_internal_deletions = 3,
|
|
extend_internal_deletions = 1529;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 3)
|
|
self.assertEqual(counts.internal_deletions, 1532)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 1535)
|
|
self.assertEqual(counts.insertions, 3)
|
|
self.assertEqual(counts.deletions, 1532)
|
|
self.assertEqual(counts.gaps, 1535)
|
|
self.assertEqual(counts.aligned, 179)
|
|
self.assertEqual(counts.identities, 172)
|
|
self.assertEqual(counts.mismatches, 7)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 5407))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr3")
|
|
self.assertEqual(alignment.query.id, "NR_111921.1")
|
|
self.assertEqual(len(alignment.target.seq), 198295559)
|
|
self.assertEqual(len(alignment.query.seq), 216)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array( [[48663767, 48663813, 48665640, 48665722, 48669098, 48669174],
|
|
[ 0, 46, 46, 128, 128, 204]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
dna = Seq(self.dna, length=len(alignment.target.seq))
|
|
alignment.target.seq = dna
|
|
alignment.query.seq = self.rna[alignment.query.id]
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.substitutions,
|
|
# fmt: off
|
|
np.array([[53., 0., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 35., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 50., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 0., 27., 0., 0., 0., 0.],
|
|
[ 9., 0., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 7., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 16., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 0., 7., 0., 0., 0., 0.],
|
|
])
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr3 48663767 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCGGTCAGTCATTGTTT
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||--------------
|
|
NR_111921 0 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCG--------------
|
|
|
|
chr3 48663827 CTATTGGCACAATGGGAGGCCCCGCCCCTCACGGCGGACTCATCGCATGGGGGAGGGGGC
|
|
60 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48663887 TCCGCGGGTTGCCGGCTAACCGTGAGAGAGTCCGGGAGGTACACTATACGGACCGGCCTC
|
|
120 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48663947 CAAAGGCGGAATCGATAACGAGCTGCAGCGCCGGGTGCAGAGGACGCGGGCATCCCGAAG
|
|
180 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664007 CCCAGGAAGAGGTCAGGGCCGGGACCCCAGAACGCTCCACAGGGTGCGGCTCCCGCGATG
|
|
240 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664067 GGGTGGATCCTGGTTCTAACAGGCGAGGAACTCCTGGCCAAGGCCTCTGGCCCGCCCCGA
|
|
300 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664127 ACGGTCCCTATGACATCACCATCAACCAATCAGTCGGCGCATCCTTTCGCCCCTTGACTG
|
|
360 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664187 CTCCGCTTCCGGGAGGCGGGGCTTCTGCGGGTTCCACCTCCCGAGCGCCCCTTGTGGCTA
|
|
420 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664247 CCAAGGTCAGGCAACAGGTGTCCAGTTGTTCCCTCTCCTGTCTACGAATCTGAGGACCTC
|
|
480 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664307 CCCAGGATCAGAGCTCTGGGCCTGATACACGGCCGGGGTTCCTACGGGTTTGTGAGTGGG
|
|
540 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664367 GGTGGAAGATCTGCAGAGGCACTTAGGGCTGAACTCCTTTGAATGGGAGCCAATCGGTGC
|
|
600 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664427 AGGGGCTGGAGGAGCGAGTCCCCCAAAGTAGttttatttatctatttagagacaaggtct
|
|
660 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664487 cactctttcggagtgcagtggtgatcacagctcaccgtagcctcgaactccccaggcgat
|
|
720 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664547 tctctcacctcagcctcccgagtagctgggactacgggtacatgtcatcacacttggcta
|
|
780 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664607 atttttgcattttttatagagacagggtctcaccatgtaggccagattagtcttgaactc
|
|
840 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664667 ctgggctcaagcaatccgcccatcttggcctcccaaagtgctgggattataggtgtgagc
|
|
900 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664727 caccgcgcccggcAACCCAGAAGTGGTTTTGACAGCAccagcgctttctgtgtccacaat
|
|
960 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664787 ctagtgagtagagggcacaaaacctgacaccacggaggcagacaggcaggggctctgccg
|
|
1020 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664847 gggaagggtgttggagtcccaaaggaggcgtctgagtcaccttcgcaacctgggacgcct
|
|
1080 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664907 tcttgcataagatgcctgagcagtgccttgaatgaccaaggggagatccgcatctgcaaa
|
|
1140 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664967 ggaagggcagggagggatagggattgggggtgggcatcctaggtcttggagactgtgtgg
|
|
1200 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665027 gcaaatgtgcagagacataaagggactatggctgagggaaatcaagCCCTGCCCTCTCAC
|
|
1260 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665087 CAATAGGGCTGGCGCTGGTCCCAGCTAACACTCCTTTTGGAGAGCAAAGCTCCTCACTTC
|
|
1320 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665147 TGAGTAGTGAGATTGATTGCGGATCACTCTCCATGTTGCTGCCTGCTGTGTGTCATCCCA
|
|
1380 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665207 CTGTCATCCTCCCTTTGTGGCTGTTCTGTGGAGCCCCTCTCCCTCAATCTGCACTCACCT
|
|
1440 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665267 CTATGCCCCAGCCCCATTGGCAGCTCCTAATGCACTCCCGGTaaaaaaaaaaaaacaaaa
|
|
1500 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665327 aCCAGATGTTAGTGATAGTGGTGGTAGTTCTTCTCTCCACCTCCAAATCTTGCCCTTGCC
|
|
1560 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665387 TCCTAATAAGACCCCTATGTGGTTTAACCTCAttttttttttttttttttttttttgaga
|
|
1620 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665447 tggagtttcactctgtcacccaggctggagtgaagtggtgtgatGGGGCTTCACCATGTg
|
|
1680 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665507 atggggcttcaccatgttggccaggctggtatcaaactcctgacctctagtgatctgccc
|
|
1740 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665567 gcctcagcctcccaaagtgctgggattaccggcatgaggcaccgtgcccagccTATCCTC
|
|
1800 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665627 CTTCTCTTATCAGCTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC
|
|
1860 -------------|||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_111921 46 -------------CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC
|
|
|
|
chr3 48665687 TGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGGGTAAGGGTGTGGCAGATACTGCCAC
|
|
1920 |||||||||||||||||||||||||||||||||||-------------------------
|
|
NR_111921 93 TGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGG-------------------------
|
|
|
|
chr3 48665747 TAACACTTCTCAGCCTTTCCTTCTCCTGCCTTTTCCACCCCACCCTGTGTTTGTCTACTC
|
|
1980 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48665807 CCAGCCAGGTGTACCTTTCCAGGGGAAGACCTGGCCAACCTGTCCAGCTCAATTAtccag
|
|
2040 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48665867 cagttctttgacctcactgagatctcgagtccattgttcatcacctcagctattgacctg
|
|
2100 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48665927 tgtcattagccttatagagttcagtgccacggaaactccctgccctgttctttttctttt
|
|
2160 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48665987 tctttttttttttttttttgagacagagccttgctctgtcgcccaggctggagtgcagtg
|
|
2220 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666047 gcgcgatctcggctcactgcaagctctgcctcccaggttcacaccattctcctgactcag
|
|
2280 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666107 cctcccgagtagctgggactacaggcgtccaccaccatgcccagctaatttttttttttg
|
|
2340 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666167 tatttttagtagagacggcgtttcaccgtgttagccaggctggtctcgatctcctgacct
|
|
2400 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666227 tgtgatgctcccgcctcggcctcccaaagtgctgggattacaggcatgagccattgtgcc
|
|
2460 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666287 cggcctgccctgttcttcttagacaaacttgctgggctaaaatctaaccccgttaaaata
|
|
2520 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666347 gactatttacgtattgtttgcctctagcgcagcagaacattgctggagaaaaacaaacaa
|
|
2580 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666407 ccgtgctaattggtctcattttatattcatgaccacaagcctcagtattatatcggaggg
|
|
2640 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666467 cctatccagtgcagtagggcaagaaaaataataagttatgaagattggaagggaaaaaaa
|
|
2700 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666527 actaattcacaagcagtaggattgtatatgtaaaaatttcaaaggaacctataggtaagt
|
|
2760 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666587 tgttagaatgagttcagcaaagttgttggacacaagatcaatatataaaaatcagttgca
|
|
2820 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666647 atttctatatgtcaccaacagttagaaaataaatttcttgcctgggcatgttggctcaag
|
|
2880 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666707 cctgtaatcccagcactttgggtggccaaggcgggcagatcacctgaggtcaggagtttg
|
|
2940 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666767 agaccagtttggccaacatggtgaaatcccgtctctactaaaaatacagaaattagccgg
|
|
3000 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666827 gcgtggtggtgggcacctgtagtcccagctactgaggaggctgaggcaggagaatcactt
|
|
3060 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666887 gaacctgggaggcagaggttgcagtgaacgagaaaaaaaaattttttttcttaaaaacaa
|
|
3120 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666947 tgatgtttacaatagcatcaagtaatatcaaatgctgaggaataaacctaatgaaagatg
|
|
3180 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667007 tgcaaagactacatacacacatacaaaaaaactataaaacattattgagggaaataaaga
|
|
3240 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667067 cataggcctggcattggtggctcatgcctgaaatctcagcactttggagggccaaggtgg
|
|
3300 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667127 gtggatcatttgaggtcaggagttagagatcagtccggccaacatggtgaaacctcatct
|
|
3360 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667187 ctactaaaaatacaaaaaaattagcttggccaggtgcagtggctcacacctgtaatccca
|
|
3420 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667247 gcactttgggaggctgaggcgggcggatcatgaggtcaggagatcgagaccatcctggct
|
|
3480 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667307 aacacggtgaaaccctgtctctactaaaaatacaaaaaaaaattagccgggcctgatggc
|
|
3540 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667367 gggcgcccgtagtcccagctactcgggaggctgaggtagcagaatggcgtgaacctggga
|
|
3600 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667427 ggtgcagcttgcagtgagcctaaattgcgccactgcactccagcctgggtaacagagcga
|
|
3660 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667487 gactccgtttcaaaaaaaaaaaaaaaaattagctgggcatgctgttgtgcacctgcaatc
|
|
3720 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667547 ccagctactctggaggatgaggcagaagtgcctgaacctgggacacagaggttgcagtga
|
|
3780 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667607 gccaagatcatgccattgcactccagcctggacaacacagccagacgctatctgaaaaaa
|
|
3840 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667667 aaaaaaaaaaaaaaagtaaaaaaaatgagaaataaagacataaataaagtgaaaaattgt
|
|
3900 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667727 tccaatattggaaaagtcaatattataaaggtgccaattttcccaaattgatatatggat
|
|
3960 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667787 tcgatgcaacttcagttaaaaatcccactaaattttggctgggtgcggtggctcacacct
|
|
4020 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667847 gtaatcccagcactttgggaggctgaggcgggcggatcacaaggtcaggagatcgagacc
|
|
4080 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667907 atcttggctaacatggtgaaaccgtctctactaaaaatacaaaagttagccgggtgtggt
|
|
4140 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667967 ggcgggcacctgtagtcccagctacttgggaggctgagacagaatggcgtgaacctgggg
|
|
4200 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668027 aggcggagcttgcagtgagccaagttgacgccactgcactccagcctgggcgacagagca
|
|
4260 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668087 agactctgtctcaaaaaaaaaaaaaaaaaaaTCCCACTAGATTTTGTGTGTGTGTAAACT
|
|
4320 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668147 GACAAACTAGATTTAGcagcctgagcaacacagcaaaaccccatctctacaaaaaataca
|
|
4380 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668207 aaaattttgcacatgcctgtatagtcccagctacttgggaggctgaagtgggaggatcat
|
|
4440 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668267 gtgagctctggggaggtcgaggctgtagtgagctatgatcacatgctgcactctagcctg
|
|
4500 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668327 ggcaacagagcaagagaccctgtatctaaaaaaagaatgaaaattaaaaaataaaaaGAa
|
|
4560 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668387 accaagattgtgtggtactggtacgaggataggaagactaaaggaacgaaatccagagac
|
|
4620 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668447 aggcctgaagatgtgtggaaacttgaattttgacaagggtgGTTCTTCAGAGCTAACATG
|
|
4680 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668507 AAGAAAGGGTTGTTTTCTTTTTTTTGTTTCCCcaggagcaactctattaactgaaagaat
|
|
4740 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668567 aggcttttcaataaatgatgctgggtcagttggatatccatatagaaaaaattaaatgag
|
|
4800 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668627 atctctatttcacactgcttgcataatcaattccatataaatttgacatctgaaaatata
|
|
4860 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668687 cagtttctagaaaacagtatTAAGACCttgttttgttttttgttgttgttgttttttgtt
|
|
4920 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668747 ttgttttttgttttttgagacagagtctcgctctgtcgccaggctggaatacagtggtgc
|
|
4980 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668807 aaccttggctcactgcaacctctgactccctagttcaagcaattctcctgcctcagcctc
|
|
5040 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668867 ccgagtagctgcgattacaggcacatgccaccacgcccagctaatttttgtatttttagt
|
|
5100 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668927 agagatgggggtttcaccatgttggccaggatggtctcgatctcctgaccctgtaatccg
|
|
5160 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668987 cccacctcggcctcccaaagtgctgggattacaggcgtgagccactgcacctggccAAGA
|
|
5220 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48669047 GAAGATCTTAAAGGTGACTTTAAGCAAACttttttttttttttttttacagagacgggag
|
|
5280 ---------------------------------------------------.........
|
|
NR_111921 128 ---------------------------------------------------AGACGGGAG
|
|
|
|
chr3 48669107 ctggagtgcagtggctgttcacaagcgtgaAAGCAAAGATTAAAAAATTTGTTTTTATAT
|
|
5340 ..............................||||||||||||||||||||||||||||||
|
|
NR_111921 137 CTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTATAT
|
|
|
|
chr3 48669167 TAAAAAA 48669174
|
|
5400 ||||||| 5407
|
|
NR_111921 197 TAAAAAA 204
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 182 chr3 198295559 + 48663767 48669174 NR_111921.1 216 + 0 204 3
|
|
46 1827 0
|
|
82 3376 0
|
|
76
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (204 aligned letters; 165 identities; 39 mismatches; 5203 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 204:
|
|
identities = 165,
|
|
mismatches = 39.
|
|
gaps = 5203:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 5203:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 5203:
|
|
open_internal_deletions = 2,
|
|
extend_internal_deletions = 5201;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 5203)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 5203)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 5203)
|
|
self.assertEqual(counts.gaps, 5203)
|
|
self.assertEqual(counts.aligned, 204)
|
|
self.assertEqual(counts.identities, 165)
|
|
self.assertEqual(counts.mismatches, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 5409))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr3")
|
|
self.assertEqual(alignment.query.id, "NR_111921.1_modified")
|
|
self.assertEqual(len(alignment.target.seq), 198295559)
|
|
self.assertEqual(len(alignment.query.seq), 220)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48663767, 48663795, 48663796, 48663813, 48665640,
|
|
48665716, 48665716, 48665722, 48669098, 48669174],
|
|
[ 3, 31, 31, 48, 48,
|
|
124, 126, 132, 132, 208]
|
|
])
|
|
# fmt: on
|
|
)
|
|
)
|
|
dna = Seq(self.dna, length=len(alignment.target))
|
|
alignment.target.seq = dna
|
|
alignment.query.seq = self.rna[alignment.query.id]
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.substitutions,
|
|
# fmt: off
|
|
np.array([[53., 0., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 34., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 2., 48., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 0., 27., 0., 0., 0., 0.],
|
|
[ 9., 0., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 7., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 16., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 0., 7., 0., 0., 0., 0.],
|
|
]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr3 48663767 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCGGTCAGTCATTGTTT
|
|
0 ||||||||||||||||||||||||||||-|||||||||||||||||--------------
|
|
NR_111921 3 CACGAGAGGAGCGGAGGCGAGGGGTGAA-GCGGAGCACTCCAATCG--------------
|
|
|
|
chr3 48663827 CTATTGGCACAATGGGAGGCCCCGCCCCTCACGGCGGACTCATCGCATGGGGGAGGGGGC
|
|
60 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48663887 TCCGCGGGTTGCCGGCTAACCGTGAGAGAGTCCGGGAGGTACACTATACGGACCGGCCTC
|
|
120 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48663947 CAAAGGCGGAATCGATAACGAGCTGCAGCGCCGGGTGCAGAGGACGCGGGCATCCCGAAG
|
|
180 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664007 CCCAGGAAGAGGTCAGGGCCGGGACCCCAGAACGCTCCACAGGGTGCGGCTCCCGCGATG
|
|
240 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664067 GGGTGGATCCTGGTTCTAACAGGCGAGGAACTCCTGGCCAAGGCCTCTGGCCCGCCCCGA
|
|
300 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664127 ACGGTCCCTATGACATCACCATCAACCAATCAGTCGGCGCATCCTTTCGCCCCTTGACTG
|
|
360 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664187 CTCCGCTTCCGGGAGGCGGGGCTTCTGCGGGTTCCACCTCCCGAGCGCCCCTTGTGGCTA
|
|
420 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664247 CCAAGGTCAGGCAACAGGTGTCCAGTTGTTCCCTCTCCTGTCTACGAATCTGAGGACCTC
|
|
480 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664307 CCCAGGATCAGAGCTCTGGGCCTGATACACGGCCGGGGTTCCTACGGGTTTGTGAGTGGG
|
|
540 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664367 GGTGGAAGATCTGCAGAGGCACTTAGGGCTGAACTCCTTTGAATGGGAGCCAATCGGTGC
|
|
600 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664427 AGGGGCTGGAGGAGCGAGTCCCCCAAAGTAGttttatttatctatttagagacaaggtct
|
|
660 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664487 cactctttcggagtgcagtggtgatcacagctcaccgtagcctcgaactccccaggcgat
|
|
720 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664547 tctctcacctcagcctcccgagtagctgggactacgggtacatgtcatcacacttggcta
|
|
780 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664607 atttttgcattttttatagagacagggtctcaccatgtaggccagattagtcttgaactc
|
|
840 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664667 ctgggctcaagcaatccgcccatcttggcctcccaaagtgctgggattataggtgtgagc
|
|
900 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664727 caccgcgcccggcAACCCAGAAGTGGTTTTGACAGCAccagcgctttctgtgtccacaat
|
|
960 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664787 ctagtgagtagagggcacaaaacctgacaccacggaggcagacaggcaggggctctgccg
|
|
1020 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664847 gggaagggtgttggagtcccaaaggaggcgtctgagtcaccttcgcaacctgggacgcct
|
|
1080 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664907 tcttgcataagatgcctgagcagtgccttgaatgaccaaggggagatccgcatctgcaaa
|
|
1140 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48664967 ggaagggcagggagggatagggattgggggtgggcatcctaggtcttggagactgtgtgg
|
|
1200 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665027 gcaaatgtgcagagacataaagggactatggctgagggaaatcaagCCCTGCCCTCTCAC
|
|
1260 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665087 CAATAGGGCTGGCGCTGGTCCCAGCTAACACTCCTTTTGGAGAGCAAAGCTCCTCACTTC
|
|
1320 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665147 TGAGTAGTGAGATTGATTGCGGATCACTCTCCATGTTGCTGCCTGCTGTGTGTCATCCCA
|
|
1380 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665207 CTGTCATCCTCCCTTTGTGGCTGTTCTGTGGAGCCCCTCTCCCTCAATCTGCACTCACCT
|
|
1440 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665267 CTATGCCCCAGCCCCATTGGCAGCTCCTAATGCACTCCCGGTaaaaaaaaaaaaacaaaa
|
|
1500 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665327 aCCAGATGTTAGTGATAGTGGTGGTAGTTCTTCTCTCCACCTCCAAATCTTGCCCTTGCC
|
|
1560 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665387 TCCTAATAAGACCCCTATGTGGTTTAACCTCAttttttttttttttttttttttttgaga
|
|
1620 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665447 tggagtttcactctgtcacccaggctggagtgaagtggtgtgatGGGGCTTCACCATGTg
|
|
1680 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665507 atggggcttcaccatgttggccaggctggtatcaaactcctgacctctagtgatctgccc
|
|
1740 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665567 gcctcagcctcccaaagtgctgggattaccggcatgaggcaccgtgcccagccTATCCTC
|
|
1800 ------------------------------------------------------------
|
|
NR_111921 48 ------------------------------------------------------------
|
|
|
|
chr3 48665627 CTTCTCTTATCAGCTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC
|
|
1860 -------------|||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_111921 48 -------------CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC
|
|
|
|
chr3 48665687 TGCTGGGCGGCAGATGGAGCGATCAGAAG--ACCAGGGTAAGGGTGTGGCAGATACTGCC
|
|
1920 |||||..||||||||||||||||||||||--||||||-----------------------
|
|
NR_111921 95 TGCTGCCCGGCAGATGGAGCGATCAGAAGCCACCAGG-----------------------
|
|
|
|
chr3 48665745 ACTAACACTTCTCAGCCTTTCCTTCTCCTGCCTTTTCCACCCCACCCTGTGTTTGTCTAC
|
|
1980 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48665805 TCCCAGCCAGGTGTACCTTTCCAGGGGAAGACCTGGCCAACCTGTCCAGCTCAATTAtcc
|
|
2040 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48665865 agcagttctttgacctcactgagatctcgagtccattgttcatcacctcagctattgacc
|
|
2100 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48665925 tgtgtcattagccttatagagttcagtgccacggaaactccctgccctgttctttttctt
|
|
2160 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48665985 tttctttttttttttttttttgagacagagccttgctctgtcgcccaggctggagtgcag
|
|
2220 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666045 tggcgcgatctcggctcactgcaagctctgcctcccaggttcacaccattctcctgactc
|
|
2280 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666105 agcctcccgagtagctgggactacaggcgtccaccaccatgcccagctaatttttttttt
|
|
2340 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666165 tgtatttttagtagagacggcgtttcaccgtgttagccaggctggtctcgatctcctgac
|
|
2400 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666225 cttgtgatgctcccgcctcggcctcccaaagtgctgggattacaggcatgagccattgtg
|
|
2460 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666285 cccggcctgccctgttcttcttagacaaacttgctgggctaaaatctaaccccgttaaaa
|
|
2520 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666345 tagactatttacgtattgtttgcctctagcgcagcagaacattgctggagaaaaacaaac
|
|
2580 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666405 aaccgtgctaattggtctcattttatattcatgaccacaagcctcagtattatatcggag
|
|
2640 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666465 ggcctatccagtgcagtagggcaagaaaaataataagttatgaagattggaagggaaaaa
|
|
2700 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666525 aaactaattcacaagcagtaggattgtatatgtaaaaatttcaaaggaacctataggtaa
|
|
2760 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666585 gttgttagaatgagttcagcaaagttgttggacacaagatcaatatataaaaatcagttg
|
|
2820 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666645 caatttctatatgtcaccaacagttagaaaataaatttcttgcctgggcatgttggctca
|
|
2880 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666705 agcctgtaatcccagcactttgggtggccaaggcgggcagatcacctgaggtcaggagtt
|
|
2940 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666765 tgagaccagtttggccaacatggtgaaatcccgtctctactaaaaatacagaaattagcc
|
|
3000 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666825 gggcgtggtggtgggcacctgtagtcccagctactgaggaggctgaggcaggagaatcac
|
|
3060 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666885 ttgaacctgggaggcagaggttgcagtgaacgagaaaaaaaaattttttttcttaaaaac
|
|
3120 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48666945 aatgatgtttacaatagcatcaagtaatatcaaatgctgaggaataaacctaatgaaaga
|
|
3180 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667005 tgtgcaaagactacatacacacatacaaaaaaactataaaacattattgagggaaataaa
|
|
3240 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667065 gacataggcctggcattggtggctcatgcctgaaatctcagcactttggagggccaaggt
|
|
3300 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667125 gggtggatcatttgaggtcaggagttagagatcagtccggccaacatggtgaaacctcat
|
|
3360 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667185 ctctactaaaaatacaaaaaaattagcttggccaggtgcagtggctcacacctgtaatcc
|
|
3420 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667245 cagcactttgggaggctgaggcgggcggatcatgaggtcaggagatcgagaccatcctgg
|
|
3480 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667305 ctaacacggtgaaaccctgtctctactaaaaatacaaaaaaaaattagccgggcctgatg
|
|
3540 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667365 gcgggcgcccgtagtcccagctactcgggaggctgaggtagcagaatggcgtgaacctgg
|
|
3600 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667425 gaggtgcagcttgcagtgagcctaaattgcgccactgcactccagcctgggtaacagagc
|
|
3660 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667485 gagactccgtttcaaaaaaaaaaaaaaaaattagctgggcatgctgttgtgcacctgcaa
|
|
3720 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667545 tcccagctactctggaggatgaggcagaagtgcctgaacctgggacacagaggttgcagt
|
|
3780 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667605 gagccaagatcatgccattgcactccagcctggacaacacagccagacgctatctgaaaa
|
|
3840 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667665 aaaaaaaaaaaaaaaaagtaaaaaaaatgagaaataaagacataaataaagtgaaaaatt
|
|
3900 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667725 gttccaatattggaaaagtcaatattataaaggtgccaattttcccaaattgatatatgg
|
|
3960 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667785 attcgatgcaacttcagttaaaaatcccactaaattttggctgggtgcggtggctcacac
|
|
4020 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667845 ctgtaatcccagcactttgggaggctgaggcgggcggatcacaaggtcaggagatcgaga
|
|
4080 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667905 ccatcttggctaacatggtgaaaccgtctctactaaaaatacaaaagttagccgggtgtg
|
|
4140 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48667965 gtggcgggcacctgtagtcccagctacttgggaggctgagacagaatggcgtgaacctgg
|
|
4200 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668025 ggaggcggagcttgcagtgagccaagttgacgccactgcactccagcctgggcgacagag
|
|
4260 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668085 caagactctgtctcaaaaaaaaaaaaaaaaaaaTCCCACTAGATTTTGTGTGTGTGTAAA
|
|
4320 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668145 CTGACAAACTAGATTTAGcagcctgagcaacacagcaaaaccccatctctacaaaaaata
|
|
4380 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668205 caaaaattttgcacatgcctgtatagtcccagctacttgggaggctgaagtgggaggatc
|
|
4440 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668265 atgtgagctctggggaggtcgaggctgtagtgagctatgatcacatgctgcactctagcc
|
|
4500 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668325 tgggcaacagagcaagagaccctgtatctaaaaaaagaatgaaaattaaaaaataaaaaG
|
|
4560 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668385 Aaaccaagattgtgtggtactggtacgaggataggaagactaaaggaacgaaatccagag
|
|
4620 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668445 acaggcctgaagatgtgtggaaacttgaattttgacaagggtgGTTCTTCAGAGCTAACA
|
|
4680 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668505 TGAAGAAAGGGTTGTTTTCTTTTTTTTGTTTCCCcaggagcaactctattaactgaaaga
|
|
4740 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668565 ataggcttttcaataaatgatgctgggtcagttggatatccatatagaaaaaattaaatg
|
|
4800 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668625 agatctctatttcacactgcttgcataatcaattccatataaatttgacatctgaaaata
|
|
4860 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668685 tacagtttctagaaaacagtatTAAGACCttgttttgttttttgttgttgttgttttttg
|
|
4920 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668745 ttttgttttttgttttttgagacagagtctcgctctgtcgccaggctggaatacagtggt
|
|
4980 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668805 gcaaccttggctcactgcaacctctgactccctagttcaagcaattctcctgcctcagcc
|
|
5040 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668865 tcccgagtagctgcgattacaggcacatgccaccacgcccagctaatttttgtattttta
|
|
5100 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668925 gtagagatgggggtttcaccatgttggccaggatggtctcgatctcctgaccctgtaatc
|
|
5160 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48668985 cgcccacctcggcctcccaaagtgctgggattacaggcgtgagccactgcacctggccAA
|
|
5220 ------------------------------------------------------------
|
|
NR_111921 132 ------------------------------------------------------------
|
|
|
|
chr3 48669045 GAGAAGATCTTAAAGGTGACTTTAAGCAAACttttttttttttttttttacagagacggg
|
|
5280 -----------------------------------------------------.......
|
|
NR_111921 132 -----------------------------------------------------AGACGGG
|
|
|
|
chr3 48669105 agctggagtgcagtggctgttcacaagcgtgaAAGCAAAGATTAAAAAATTTGTTTTTAT
|
|
5340 ................................||||||||||||||||||||||||||||
|
|
NR_111921 139 AGCTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTAT
|
|
|
|
chr3 48669165 ATTAAAAAA 48669174
|
|
5400 ||||||||| 5409
|
|
NR_111921 199 ATTAAAAAA 208
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 175 chr3 198295559 + 48663767 48669174 NR_111921.1_modified 220 + 3 208 4
|
|
28 1 0
|
|
17 1827 0
|
|
76 0 2
|
|
6 3376 0
|
|
76
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (203 aligned letters; 162 identities; 41 mismatches; 5206 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 203:
|
|
identities = 162,
|
|
mismatches = 41.
|
|
gaps = 5206:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 5206:
|
|
internal_insertions = 2:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 1;
|
|
internal_deletions = 5204:
|
|
open_internal_deletions = 3,
|
|
extend_internal_deletions = 5201;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 2)
|
|
self.assertEqual(counts.internal_deletions, 5204)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 5206)
|
|
self.assertEqual(counts.insertions, 2)
|
|
self.assertEqual(counts.deletions, 5204)
|
|
self.assertEqual(counts.gaps, 5206)
|
|
self.assertEqual(counts.aligned, 203)
|
|
self.assertEqual(counts.identities, 162)
|
|
self.assertEqual(counts.mismatches, 41)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_reading(self):
|
|
"""Test parsing dna_rna.chain."""
|
|
path = "Blat/dna_rna.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
self.check_alignments(alignments)
|
|
alignments = iter(alignments)
|
|
self.check_alignments(alignments)
|
|
with Align.parse(path, "chain") as alignments:
|
|
self.check_alignments(alignments)
|
|
with self.assertRaises(AttributeError):
|
|
alignments._stream
|
|
with Align.parse(path, "chain") as alignments:
|
|
pass
|
|
with self.assertRaises(AttributeError):
|
|
alignments._stream
|
|
with open(path) as stream:
|
|
data = stream.read()
|
|
stream = NamedTemporaryFile("w+t")
|
|
stream.write(data)
|
|
stream.seek(0)
|
|
alignments = Align.parse(stream, "chain")
|
|
self.check_alignments(alignments)
|
|
|
|
def test_writing(self):
|
|
"""Test writing the alignments in dna_rna.chain."""
|
|
path = "Blat/dna_rna.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "chain")
|
|
self.assertEqual(n, 4)
|
|
stream.seek(0)
|
|
alignments = Align.parse(stream, "chain")
|
|
self.check_alignments(alignments)
|
|
|
|
|
|
class TestAlign_dna(unittest.TestCase):
|
|
queries = {
|
|
record.id: str(record.seq)
|
|
for record in SeqIO.parse("Blat/fasta_34.fa", "fasta")
|
|
}
|
|
|
|
def test_reading_psl_34_001(self):
|
|
"""Test parsing psl_34_001.chain."""
|
|
# The chain file psl_34_001.chain was generated from the PSL file using:
|
|
# pslToChain psl_34_001.psl psl_34_001.chain
|
|
path = "Blat/psl_34_001.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
self.check_reading_psl_34_001(alignments)
|
|
|
|
def check_reading_psl_34_001(self, alignments):
|
|
"""Check parsing psl_34_001.chain."""
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 16))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 191154276)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 61646095 ???????????????? 61646111
|
|
0 |||||||||||||||| 16
|
|
hg18_dna 11 ???????????????? 27
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61646095, 61646111],
|
|
[ 11, 27]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 16 chr4 191154276 + 61646095 61646111 hg18_dna 33 + 11 27 1
|
|
16
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (16 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 16:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 16)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 33))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 10271783 ????????????????????????????????? 10271816
|
|
0 ||||||||||||||||||||||||||||||||| 33
|
|
hg18_dna 0 ????????????????????????????????? 33
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[10271783, 10271816],
|
|
[ 0, 33]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr1 249250621 + 10271783 10271816 hg18_dna 33 + 0 33 2
|
|
33
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (33 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 33:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 33)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 17))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 53575980 ????????????????? 53575997
|
|
0 ||||||||||||||||| 17
|
|
hg18_dna 25 ????????????????? 8
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[53575980, 53575997],
|
|
[ 25, 8]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 17 chr2 243199373 + 53575980 53575997 hg18_dna 33 - 8 25 3
|
|
17
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (17 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 17:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 17)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr9")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 141213431)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr9 85737865 ????????????????????????????????????????? 85737906
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 9 ????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[85737865, 85737906],
|
|
[ 9, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 35 chr9 141213431 + 85737865 85737906 hg19_dna 50 + 9 50 4
|
|
41
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 41:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr8")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 146364022)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr8 95160479 ????????????????????????????????????????? 95160520
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 8 ????????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[95160479, 95160520],
|
|
[ 8, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr8 146364022 + 95160479 95160520 hg19_dna 50 + 8 49 5
|
|
41
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 41:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 51304566)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 42144400 ???????????????????????????????????? 42144436
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 11 ???????????????????????????????????? 47
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[42144400, 42144436],
|
|
[ 11, 47]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 30 chr22 51304566 + 42144400 42144436 hg19_dna 50 + 11 47 6
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 48))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 183925984 ??????----?????????????????????????????????????? 183926028
|
|
0 ||||||----|||||||||||||||||||||||||||||||||||||| 48
|
|
hg19_dna 1 ???????????????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[183925984, 183925990, 183925990, 183926028],
|
|
[ 1, 7, 11, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr2 243199373 + 183925984 183926028 hg19_dna 50 + 1 49 7
|
|
6 0 4
|
|
38
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 44:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 4:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 4:
|
|
internal_insertions = 4:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 3;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 4)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 4)
|
|
self.assertEqual(counts.insertions, 4)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 4)
|
|
self.assertEqual(counts.aligned, 44)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 170))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 35483340 ????????????????????????????????????????????????????????????
|
|
0 |||||||||||||||||||||||||-----------------------------------
|
|
hg19_dna 10 ?????????????????????????-----------------------------------
|
|
|
|
chr19 35483400 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
hg19_dna 35 ------------------------------------------------------------
|
|
|
|
chr19 35483460 ?????????????????????????????????????????????????? 35483510
|
|
120 ---------------------------------------||||||||||| 170
|
|
hg19_dna 35 ---------------------------------------??????????? 46
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[35483340, 35483365, 35483499, 35483510],
|
|
[ 10, 35, 35, 46]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 31 chr19 59128983 + 35483340 35483510 hg19_dna 50 + 10 46 8
|
|
25 134 0
|
|
11
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 134 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 134:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 134:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 134:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 133;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 134)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 134)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 134)
|
|
self.assertEqual(counts.gaps, 134)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 78077248)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 23891310 ??????????????????????????????????????? 23891349
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 10 ??????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[23891310, 23891349],
|
|
[ 10, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 39 chr18 78077248 + 23891310 23891349 hg19_dna 50 + 10 49 9
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 28))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 78077248)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 43252217 ???????????????????????????? 43252245
|
|
0 |||||||||||||||||||||||||||| 28
|
|
hg19_dna 21 ???????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[43252217, 43252245],
|
|
[ 21, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 26 chr18 78077248 + 43252217 43252245 hg19_dna 50 + 21 49 10
|
|
28
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 28:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 54))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 115169878)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 52759147 ?????????????---??????????????????????????????????????
|
|
0 |||||||---------||||||||||||||||||||||||||||||||||||||
|
|
hg19_dna 1 ???????------?????????????????????????????????????????
|
|
|
|
chr13 52759198
|
|
54
|
|
hg19_dna 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[52759147, 52759154, 52759160, 52759160, 52759198],
|
|
[ 1, 8, 8, 11, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr13 115169878 + 52759147 52759198 hg19_dna 50 + 1 49 11
|
|
7 6 3
|
|
38
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (45 aligned letters; 0 identities; 0 mismatches; 9 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 45:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 9:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 9:
|
|
internal_insertions = 3:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 2;
|
|
internal_deletions = 6:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 5;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 3)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 9)
|
|
self.assertEqual(counts.insertions, 3)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 9)
|
|
self.assertEqual(counts.aligned, 45)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 50))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 1207056 ?????????????????????????????????????????????????? 1207106
|
|
0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50
|
|
hg19_dna 0 ?????????????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[1207056, 1207106],
|
|
[ 0, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 50 chr1 249250621 + 1207056 1207106 hg19_dna 50 + 0 50 12
|
|
50
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (50 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 50:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 50)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 61700837 ?????????????????????????????????? 61700871
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 1 ?????????????????????????????????? 35
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61700837, 61700871],
|
|
[ 1, 35]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 28 chr1 249250621 + 61700837 61700871 hg19_dna 50 + 1 35 13
|
|
34
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 34:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 44))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 191154276)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 37558157 ????????????????----------?????????????????? 37558191
|
|
0 ||||||||||----------------|||||||||||||||||| 44
|
|
hg19_dna 49 ??????????------???????????????????????????? 11
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[37558157, 37558167, 37558173, 37558173, 37558191],
|
|
[ 49, 39, 39, 29, 11]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "psl"),
|
|
"""\
|
|
28 0 0 0 1 10 1 6 - hg19_dna 50 11 49 chr4 191154276 37558157 37558191 2 10,18, 1,21, 37558157,37558173,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 16 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 28:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 16:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 16:
|
|
internal_insertions = 10:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 9;
|
|
internal_deletions = 6:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 5;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 10)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 16)
|
|
self.assertEqual(counts.insertions, 10)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 16)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 37))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 51304566)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 48997405 ????????????????????????????????????? 48997442
|
|
0 ||||||||||||||||||||||||||||||||||||| 37
|
|
hg19_dna 49 ????????????????????????????????????? 12
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48997405, 48997442],
|
|
[ 49, 12]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr22 51304566 + 48997405 48997442 hg19_dna 50 - 1 38 15
|
|
37
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (37 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 37:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 37)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 120641740 ???????????????????????????????????? 120641776
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[120641740, 120641776],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 34 chr2 243199373 + 120641740 120641776 hg19_dna 50 - 1 37 16
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 54017130 ??????????????????????????????????????? 54017169
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 49 ??????????????????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[54017130, 54017169],
|
|
[ 49, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 39 chr19 59128983 + 54017130 54017169 hg19_dna 50 - 1 40 17
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 553742 ??????????????????????????????????????? 553781
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 49 ??????????????????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[553742, 553781],
|
|
[ 49, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr19 59128983 + 553742 553781 hg19_dna 50 - 1 40 18
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 135534747)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 99388555 ???????????????????????????????????? 99388591
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[99388555, 99388591],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 30 chr10 135534747 + 99388555 99388591 hg19_dna 50 - 1 37 19
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 25))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 135534747)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 112178171 ????????????????????????? 112178196
|
|
0 ||||||||||||||||||||||||| 25
|
|
hg19_dna 35 ????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[112178171, 112178196],
|
|
[ 35, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 23 chr10 135534747 + 112178171 112178196 hg19_dna 50 - 15 40 20
|
|
25
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (25 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 25:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 25)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 39368490 ???????????????????????????????????? 39368526
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[39368490, 39368526],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 34 chr1 249250621 + 39368490 39368526 hg19_dna 50 - 1 37 21
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 220325687 ?????????????????????????????????? 220325721
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 47 ?????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[220325687, 220325721],
|
|
[ 47, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 32 chr1 249250621 + 220325687 220325721 hg19_dna 50 - 3 37 22
|
|
34
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 34:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_chain_34_001(self):
|
|
"""Test writing the alignments in psl_34_001.chain."""
|
|
path = "Blat/psl_34_001.chain"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "chain")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "chain")
|
|
self.assertEqual(n, 22)
|
|
stream.seek(0)
|
|
alignments = Align.parse(stream, "chain")
|
|
self.check_reading_psl_34_001(alignments)
|
|
|
|
def test_reading_chain_34_002(self):
|
|
"""Test parsing psl_34_002.chain."""
|
|
# The chain file psl_34_002.chain was generated from the PSL file using:
|
|
# pslToChain psl_34_002.psl psl_34_002.chain
|
|
path = "Blat/psl_34_002.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_34_002(self):
|
|
"""Test writing the alignments in psl_34_002.chain."""
|
|
path = "Blat/psl_34_002.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "chain")
|
|
self.assertEqual(n, 0)
|
|
stream.seek(0)
|
|
alignments = Align.parse(stream, "chain")
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_reading_psl_34_003(self):
|
|
"""Test parsing psl_34_003.chain."""
|
|
# The chain file psl_34_003.chain was generated from the PSL file using:
|
|
# pslToChain psl_34_003.psl psl_34_003.chain
|
|
path = "Blat/psl_34_003.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
self.check_reading_psl_34_003(alignments)
|
|
|
|
def check_reading_psl_34_003(self, alignments):
|
|
"""Check parsing psl_34_003.chain."""
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 16))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 191154276)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 61646095 ???????????????? 61646111
|
|
0 |||||||||||||||| 16
|
|
hg18_dna 11 ???????????????? 27
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61646095, 61646111],
|
|
[ 11, 27]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 16 chr4 191154276 + 61646095 61646111 hg18_dna 33 + 11 27 1
|
|
16
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (16 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 16:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 16)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 33))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 10271783 ????????????????????????????????? 10271816
|
|
0 ||||||||||||||||||||||||||||||||| 33
|
|
hg18_dna 0 ????????????????????????????????? 33
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[10271783, 10271816],
|
|
[ 0, 33]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr1 249250621 + 10271783 10271816 hg18_dna 33 + 0 33 2
|
|
33
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (33 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 33:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 33)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 17))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 53575980 ????????????????? 53575997
|
|
0 ||||||||||||||||| 17
|
|
hg18_dna 25 ????????????????? 8
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[53575980, 53575997],
|
|
[ 25, 8]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 17 chr2 243199373 + 53575980 53575997 hg18_dna 33 - 8 25 3
|
|
17
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (17 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 17:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 17)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_34_003(self):
|
|
"""Test writing the alignments in psl_34_003.chain."""
|
|
path = "Blat/psl_34_003.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "chain")
|
|
self.assertEqual(n, 3)
|
|
stream.seek(0)
|
|
alignments = Align.parse(stream, "chain")
|
|
self.check_reading_psl_34_003(alignments)
|
|
|
|
def test_reading_psl_34_004(self):
|
|
"""Test parsing psl_34_004.chain."""
|
|
# The chain file psl_34_004.chain was generated from the PSL file using:
|
|
# pslToChain psl_34_004.psl psl_34_004.chain
|
|
path = "Blat/psl_34_004.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
self.check_reading_psl_34_004(alignments)
|
|
|
|
def check_reading_psl_34_004(self, alignments):
|
|
"""Check parsing psl_34_004.chain."""
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr9")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 141213431)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr9 85737865 ????????????????????????????????????????? 85737906
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 9 ????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[85737865, 85737906],
|
|
[ 9, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 35 chr9 141213431 + 85737865 85737906 hg19_dna 50 + 9 50 1
|
|
41
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 41:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr8")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 146364022)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr8 95160479 ????????????????????????????????????????? 95160520
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 8 ????????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[95160479, 95160520],
|
|
[ 8, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr8 146364022 + 95160479 95160520 hg19_dna 50 + 8 49 2
|
|
41
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 41:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 51304566)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 42144400 ???????????????????????????????????? 42144436
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 11 ???????????????????????????????????? 47
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[42144400, 42144436],
|
|
[ 11, 47]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 30 chr22 51304566 + 42144400 42144436 hg19_dna 50 + 11 47 3
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 48))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 183925984 ??????----?????????????????????????????????????? 183926028
|
|
0 ||||||----|||||||||||||||||||||||||||||||||||||| 48
|
|
hg19_dna 1 ???????????????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[183925984, 183925990, 183925990, 183926028],
|
|
[ 1, 7, 11, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr2 243199373 + 183925984 183926028 hg19_dna 50 + 1 49 4
|
|
6 0 4
|
|
38
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 44:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 4:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 4:
|
|
internal_insertions = 4:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 3;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 4)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 4)
|
|
self.assertEqual(counts.insertions, 4)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 4)
|
|
self.assertEqual(counts.aligned, 44)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 170))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 35483340 ????????????????????????????????????????????????????????????
|
|
0 |||||||||||||||||||||||||-----------------------------------
|
|
hg19_dna 10 ?????????????????????????-----------------------------------
|
|
|
|
chr19 35483400 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
hg19_dna 35 ------------------------------------------------------------
|
|
|
|
chr19 35483460 ?????????????????????????????????????????????????? 35483510
|
|
120 ---------------------------------------||||||||||| 170
|
|
hg19_dna 35 ---------------------------------------??????????? 46
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[35483340, 35483365, 35483499, 35483510],
|
|
[ 10, 35, 35, 46]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 31 chr19 59128983 + 35483340 35483510 hg19_dna 50 + 10 46 5
|
|
25 134 0
|
|
11
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 134 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 134:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 134:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 134:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 133;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 134)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 134)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 134)
|
|
self.assertEqual(counts.gaps, 134)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 78077248)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 23891310 ??????????????????????????????????????? 23891349
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 10 ??????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[23891310, 23891349],
|
|
[ 10, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 39 chr18 78077248 + 23891310 23891349 hg19_dna 50 + 10 49 6
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 28))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 78077248)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 43252217 ???????????????????????????? 43252245
|
|
0 |||||||||||||||||||||||||||| 28
|
|
hg19_dna 21 ???????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[43252217, 43252245],
|
|
[ 21, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 26 chr18 78077248 + 43252217 43252245 hg19_dna 50 + 21 49 7
|
|
28
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 28:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 54))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 115169878)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 52759147 ?????????????---??????????????????????????????????????
|
|
0 |||||||---------||||||||||||||||||||||||||||||||||||||
|
|
hg19_dna 1 ???????------?????????????????????????????????????????
|
|
|
|
chr13 52759198
|
|
54
|
|
hg19_dna 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[52759147, 52759154, 52759160, 52759160, 52759198],
|
|
[ 1, 8, 8, 11, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr13 115169878 + 52759147 52759198 hg19_dna 50 + 1 49 8
|
|
7 6 3
|
|
38
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (45 aligned letters; 0 identities; 0 mismatches; 9 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 45:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 9:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 9:
|
|
internal_insertions = 3:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 2;
|
|
internal_deletions = 6:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 5;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 3)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 9)
|
|
self.assertEqual(counts.insertions, 3)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 9)
|
|
self.assertEqual(counts.aligned, 45)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 50))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 1207056 ?????????????????????????????????????????????????? 1207106
|
|
0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50
|
|
hg19_dna 0 ?????????????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[1207056, 1207106],
|
|
[ 0, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 50 chr1 249250621 + 1207056 1207106 hg19_dna 50 + 0 50 9
|
|
50
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (50 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 50:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 50)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 61700837 ?????????????????????????????????? 61700871
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 1 ?????????????????????????????????? 35
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61700837, 61700871],
|
|
[ 1, 35]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 28 chr1 249250621 + 61700837 61700871 hg19_dna 50 + 1 35 10
|
|
34
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 34:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 44))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 191154276)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 37558157 ????????????????----------?????????????????? 37558191
|
|
0 ||||||||||----------------|||||||||||||||||| 44
|
|
hg19_dna 49 ??????????------???????????????????????????? 11
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[37558157, 37558167, 37558173, 37558173, 37558191],
|
|
[ 49, 39, 39, 29, 11]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 26 chr4 191154276 + 37558157 37558191 hg19_dna 50 - 1 39 11
|
|
10 6 10
|
|
18
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 16 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 28:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 16:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 16:
|
|
internal_insertions = 10:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 9;
|
|
internal_deletions = 6:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 5;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 10)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 16)
|
|
self.assertEqual(counts.insertions, 10)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 16)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 37))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 51304566)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 48997405 ????????????????????????????????????? 48997442
|
|
0 ||||||||||||||||||||||||||||||||||||| 37
|
|
hg19_dna 49 ????????????????????????????????????? 12
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48997405, 48997442],
|
|
[ 49, 12]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr22 51304566 + 48997405 48997442 hg19_dna 50 - 1 38 12
|
|
37
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (37 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 37:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 37)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 120641740 ???????????????????????????????????? 120641776
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[120641740, 120641776],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 34 chr2 243199373 + 120641740 120641776 hg19_dna 50 - 1 37 13
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 54017130 ??????????????????????????????????????? 54017169
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 49 ??????????????????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[54017130, 54017169],
|
|
[ 49, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 39 chr19 59128983 + 54017130 54017169 hg19_dna 50 - 1 40 14
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 553742 ??????????????????????????????????????? 553781
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 49 ??????????????????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[553742, 553781],
|
|
[ 49, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr19 59128983 + 553742 553781 hg19_dna 50 - 1 40 15
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 135534747)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 99388555 ???????????????????????????????????? 99388591
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[99388555, 99388591],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 30 chr10 135534747 + 99388555 99388591 hg19_dna 50 - 1 37 16
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 25))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 135534747)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 112178171 ????????????????????????? 112178196
|
|
0 ||||||||||||||||||||||||| 25
|
|
hg19_dna 35 ????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[112178171, 112178196],
|
|
[ 35, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 23 chr10 135534747 + 112178171 112178196 hg19_dna 50 - 15 40 17
|
|
25
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (25 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 25:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 25)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 39368490 ???????????????????????????????????? 39368526
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[39368490, 39368526],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 34 chr1 249250621 + 39368490 39368526 hg19_dna 50 - 1 37 18
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 220325687 ?????????????????????????????????? 220325721
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 47 ?????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[220325687, 220325721],
|
|
[ 47, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 32 chr1 249250621 + 220325687 220325721 hg19_dna 50 - 3 37 19
|
|
34
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 34:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_34_004(self):
|
|
"""Test writing the alignments in psl_34_004.chain."""
|
|
path = "Blat/psl_34_004.chain"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "chain")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "chain")
|
|
self.assertEqual(n, 19)
|
|
stream.seek(0)
|
|
alignments = Align.parse(stream, "chain")
|
|
self.check_reading_psl_34_004(alignments)
|
|
|
|
def test_reading_psl_34_005(self):
|
|
"""Test parsing psl_34_005.chain."""
|
|
# The chain file psl_34_005.chain was generated from the PSL file using:
|
|
# pslToChain psl_34_005.psl psl_34_005.chain
|
|
path = "Blat/psl_34_005.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
self.check_reading_psl_34_005(alignments)
|
|
|
|
def check_reading_psl_34_005(self, alignments):
|
|
"""Check parsing psl_34_005.chain."""
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 16))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 191154276)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 61646095 ???????????????? 61646111
|
|
0 |||||||||||||||| 16
|
|
hg18_dna 11 ???????????????? 27
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61646095, 61646111],
|
|
[ 11, 27]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 16 chr4 191154276 + 61646095 61646111 hg18_dna 33 + 11 27 1
|
|
16
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (16 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 16:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 16)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 33))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 10271783 ????????????????????????????????? 10271816
|
|
0 ||||||||||||||||||||||||||||||||| 33
|
|
hg18_dna 0 ????????????????????????????????? 33
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[10271783, 10271816],
|
|
[ 0, 33]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr1 249250621 + 10271783 10271816 hg18_dna 33 + 0 33 2
|
|
33
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (33 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 33:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 33)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 17))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 33)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 53575980 ????????????????? 53575997
|
|
0 ||||||||||||||||| 17
|
|
hg18_dna 25 ????????????????? 8
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[53575980, 53575997],
|
|
[ 25, 8]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 17 chr2 243199373 + 53575980 53575997 hg18_dna 33 - 8 25 3
|
|
17
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (17 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 17:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 17)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr9")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 141213431)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr9 85737865 ????????????????????????????????????????? 85737906
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 9 ????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[85737865, 85737906],
|
|
[ 9, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 35 chr9 141213431 + 85737865 85737906 hg19_dna 50 + 9 50 4
|
|
41
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 41:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr8")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 146364022)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr8 95160479 ????????????????????????????????????????? 95160520
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 8 ????????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[95160479, 95160520],
|
|
[ 8, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr8 146364022 + 95160479 95160520 hg19_dna 50 + 8 49 5
|
|
41
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (41 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 41:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 51304566)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 42144400 ???????????????????????????????????? 42144436
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 11 ???????????????????????????????????? 47
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[42144400, 42144436],
|
|
[ 11, 47]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 30 chr22 51304566 + 42144400 42144436 hg19_dna 50 + 11 47 6
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 48))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 183925984 ??????----?????????????????????????????????????? 183926028
|
|
0 ||||||----|||||||||||||||||||||||||||||||||||||| 48
|
|
hg19_dna 1 ???????????????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[183925984, 183925990, 183925990, 183926028],
|
|
[ 1, 7, 11, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr2 243199373 + 183925984 183926028 hg19_dna 50 + 1 49 7
|
|
6 0 4
|
|
38
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (44 aligned letters; 0 identities; 0 mismatches; 4 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 44:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 4:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 4:
|
|
internal_insertions = 4:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 3;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 4)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 4)
|
|
self.assertEqual(counts.insertions, 4)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 4)
|
|
self.assertEqual(counts.aligned, 44)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 170))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 35483340 ????????????????????????????????????????????????????????????
|
|
0 |||||||||||||||||||||||||-----------------------------------
|
|
hg19_dna 10 ?????????????????????????-----------------------------------
|
|
|
|
chr19 35483400 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
hg19_dna 35 ------------------------------------------------------------
|
|
|
|
chr19 35483460 ?????????????????????????????????????????????????? 35483510
|
|
120 ---------------------------------------||||||||||| 170
|
|
hg19_dna 35 ---------------------------------------??????????? 46
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[35483340, 35483365, 35483499, 35483510],
|
|
[ 10, 35, 35, 46]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 31 chr19 59128983 + 35483340 35483510 hg19_dna 50 + 10 46 8
|
|
25 134 0
|
|
11
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 134 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 134:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 134:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 134:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 133;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 134)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 134)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 134)
|
|
self.assertEqual(counts.gaps, 134)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 78077248)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 23891310 ??????????????????????????????????????? 23891349
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 10 ??????????????????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[23891310, 23891349],
|
|
[ 10, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 39 chr18 78077248 + 23891310 23891349 hg19_dna 50 + 10 49 9
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 28))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 78077248)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 43252217 ???????????????????????????? 43252245
|
|
0 |||||||||||||||||||||||||||| 28
|
|
hg19_dna 21 ???????????????????????????? 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[43252217, 43252245],
|
|
[ 21, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 26 chr18 78077248 + 43252217 43252245 hg19_dna 50 + 21 49 10
|
|
28
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 28:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 54))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 115169878)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 52759147 ?????????????---??????????????????????????????????????
|
|
0 |||||||---------||||||||||||||||||||||||||||||||||||||
|
|
hg19_dna 1 ???????------?????????????????????????????????????????
|
|
|
|
chr13 52759198
|
|
54
|
|
hg19_dna 49
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[52759147, 52759154, 52759160, 52759160, 52759198],
|
|
[ 1, 8, 8, 11, 49]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 41 chr13 115169878 + 52759147 52759198 hg19_dna 50 + 1 49 11
|
|
7 6 3
|
|
38
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (45 aligned letters; 0 identities; 0 mismatches; 9 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 45:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 9:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 9:
|
|
internal_insertions = 3:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 2;
|
|
internal_deletions = 6:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 5;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 3)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 9)
|
|
self.assertEqual(counts.insertions, 3)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 9)
|
|
self.assertEqual(counts.aligned, 45)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 50))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 1207056 ?????????????????????????????????????????????????? 1207106
|
|
0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50
|
|
hg19_dna 0 ?????????????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[1207056, 1207106],
|
|
[ 0, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 50 chr1 249250621 + 1207056 1207106 hg19_dna 50 + 0 50 12
|
|
50
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (50 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 50:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 50)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 61700837 ?????????????????????????????????? 61700871
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 1 ?????????????????????????????????? 35
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61700837, 61700871],
|
|
[ 1, 35]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 28 chr1 249250621 + 61700837 61700871 hg19_dna 50 + 1 35 13
|
|
34
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 34:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 44))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 191154276)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 37558157 ????????????????----------?????????????????? 37558191
|
|
0 ||||||||||----------------|||||||||||||||||| 44
|
|
hg19_dna 49 ??????????------???????????????????????????? 11
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[37558157, 37558167, 37558173, 37558173, 37558191],
|
|
[ 49, 39, 39, 29, 11]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 26 chr4 191154276 + 37558157 37558191 hg19_dna 50 - 1 39 14
|
|
10 6 10
|
|
18
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (28 aligned letters; 0 identities; 0 mismatches; 16 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 28:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 16:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 16:
|
|
internal_insertions = 10:
|
|
open_internal_insertions = 1,
|
|
extend_internal_insertions = 9;
|
|
internal_deletions = 6:
|
|
open_internal_deletions = 1,
|
|
extend_internal_deletions = 5;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 10)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 16)
|
|
self.assertEqual(counts.insertions, 10)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 16)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 37))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 51304566)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 48997405 ????????????????????????????????????? 48997442
|
|
0 ||||||||||||||||||||||||||||||||||||| 37
|
|
hg19_dna 49 ????????????????????????????????????? 12
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48997405, 48997442],
|
|
[ 49, 12]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr22 51304566 + 48997405 48997442 hg19_dna 50 - 1 38 15
|
|
37
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (37 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 37:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 37)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 243199373)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 120641740 ???????????????????????????????????? 120641776
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[120641740, 120641776],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 34 chr2 243199373 + 120641740 120641776 hg19_dna 50 - 1 37 16
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 54017130 ??????????????????????????????????????? 54017169
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 49 ??????????????????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[54017130, 54017169],
|
|
[ 49, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 39 chr19 59128983 + 54017130 54017169 hg19_dna 50 - 1 40 17
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 59128983)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 553742 ??????????????????????????????????????? 553781
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 49 ??????????????????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[553742, 553781],
|
|
[ 49, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 33 chr19 59128983 + 553742 553781 hg19_dna 50 - 1 40 18
|
|
39
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (39 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 39:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 135534747)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 99388555 ???????????????????????????????????? 99388591
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[99388555, 99388591],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 30 chr10 135534747 + 99388555 99388591 hg19_dna 50 - 1 37 19
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 25))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 135534747)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 112178171 ????????????????????????? 112178196
|
|
0 ||||||||||||||||||||||||| 25
|
|
hg19_dna 35 ????????????????????????? 10
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[112178171, 112178196],
|
|
[ 35, 10]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 23 chr10 135534747 + 112178171 112178196 hg19_dna 50 - 15 40 20
|
|
25
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (25 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 25:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 25)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 39368490 ???????????????????????????????????? 39368526
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 49 ???????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[39368490, 39368526],
|
|
[ 49, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 34 chr1 249250621 + 39368490 39368526 hg19_dna 50 - 1 37 21
|
|
36
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (36 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 36:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertEqual(len(alignment.target.seq), 249250621)
|
|
self.assertEqual(len(alignment.query.seq), 50)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 220325687 ?????????????????????????????????? 220325721
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 47 ?????????????????????????????????? 13
|
|
""",
|
|
)
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[220325687, 220325721],
|
|
[ 47, 13]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "chain"),
|
|
"""\
|
|
chain 32 chr1 249250621 + 220325687 220325721 hg19_dna 50 - 3 37 22
|
|
34
|
|
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(
|
|
repr(counts),
|
|
"<AlignmentCounts object (34 aligned letters; 0 identities; 0 mismatches; 0 gaps) at 0x%x>"
|
|
% id(counts),
|
|
)
|
|
self.assertEqual(
|
|
str(counts),
|
|
"""\
|
|
AlignmentCounts object with
|
|
aligned = 34:
|
|
identities = 0,
|
|
mismatches = 0.
|
|
gaps = 0:
|
|
left_gaps = 0:
|
|
left_insertions = 0:
|
|
open_left_insertions = 0,
|
|
extend_left_insertions = 0;
|
|
left_deletions = 0:
|
|
open_left_deletions = 0,
|
|
extend_left_deletions = 0;
|
|
internal_gaps = 0:
|
|
internal_insertions = 0:
|
|
open_internal_insertions = 0,
|
|
extend_internal_insertions = 0;
|
|
internal_deletions = 0:
|
|
open_internal_deletions = 0,
|
|
extend_internal_deletions = 0;
|
|
right_gaps = 0:
|
|
right_insertions = 0:
|
|
open_right_insertions = 0,
|
|
extend_right_insertions = 0;
|
|
right_deletions = 0:
|
|
open_right_deletions = 0,
|
|
extend_right_deletions = 0.
|
|
""",
|
|
)
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_34_005(self):
|
|
"""Test writing the alignments in psl_34_005.chain."""
|
|
path = "Blat/psl_34_005.chain"
|
|
alignments = Align.parse(path, "chain")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "chain")
|
|
self.assertEqual(n, 22)
|
|
stream.seek(0)
|
|
alignments = Align.parse(stream, "chain")
|
|
self.check_reading_psl_34_005(alignments)
|
|
|
|
|
|
class TestAlign_strand(unittest.TestCase):
|
|
def test_format(self):
|
|
"""Test alignment with the target on the opposite strand."""
|
|
sequences = ["AACAGCAGCGTGTCG", "CAGCTAGCGAA"]
|
|
coordinates = np.array(
|
|
[[0, 2, 2, 3, 4, 6, 6, 9, 10, 12, 15], [11, 11, 9, 8, 8, 6, 5, 2, 2, 0, 0]]
|
|
)
|
|
score = 8
|
|
alignment = Alignment(sequences, coordinates)
|
|
alignment.score = score
|
|
chain1 = """\
|
|
chain 8 target 15 + 0 15 query 11 - 0 11
|
|
0 2 2
|
|
1 1 0
|
|
2 0 1
|
|
3 1 0
|
|
0 3 0
|
|
2
|
|
|
|
"""
|
|
chain2 = """\
|
|
chain 8 target 15 - 0 15 query 11 + 0 11
|
|
2 3 0
|
|
3 1 0
|
|
2 0 1
|
|
1 1 0
|
|
0 2 2
|
|
0
|
|
|
|
"""
|
|
chain3 = """\
|
|
chain 8 target 15 + 0 15 query 11 - 0 11
|
|
2 3 0
|
|
3 1 0
|
|
2 0 1
|
|
1 1 0
|
|
0 2 2
|
|
0
|
|
|
|
"""
|
|
chain4 = """\
|
|
chain 8 target 15 - 0 15 query 11 + 0 11
|
|
0 2 2
|
|
1 1 0
|
|
2 0 1
|
|
3 1 0
|
|
0 3 0
|
|
2
|
|
|
|
"""
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
target 0 AA--CAGC-AGCGTGTCG 15
|
|
0 ----|-||-|||-||--- 18
|
|
query 11 --TTC-GCTAGC-TG--- 0
|
|
""",
|
|
)
|
|
self.assertEqual(format(alignment, "chain"), chain1)
|
|
alignment.coordinates = alignment.coordinates[:, ::-1]
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
target 15 CGACACGCT-GCTG--TT 0
|
|
0 ---||-|||-||-|---- 18
|
|
query 0 ---CA-GCTAGC-GAA-- 11
|
|
""",
|
|
)
|
|
self.assertEqual(format(alignment, "chain"), chain2)
|
|
alignment.coordinates = alignment.coordinates[:, ::-1]
|
|
alignment = alignment.reverse_complement()
|
|
alignment.score = score
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
target 0 CGACACGCT-GCTG--TT 15
|
|
0 ---||-|||-||-|---- 18
|
|
query 11 ---CA-GCTAGC-GAA-- 0
|
|
""",
|
|
)
|
|
self.assertEqual(format(alignment, "chain"), chain3)
|
|
alignment.coordinates = alignment.coordinates[:, ::-1]
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
target 15 AA--CAGC-AGCGTGTCG 0
|
|
0 ----|-||-|||-||--- 18
|
|
query 0 --TTC-GCTAGC-TG--- 11
|
|
""",
|
|
)
|
|
self.assertEqual(format(alignment, "chain"), chain4)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
runner = unittest.TextTestRunner(verbosity=2)
|
|
unittest.main(testRunner=runner)
|