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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
155 lines
6.5 KiB
Python
155 lines
6.5 KiB
Python
# Copyright 2001 by Iddo Friedberg. 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 CAPS module."""
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import unittest
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from Bio import CAPS
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from Bio.Align import Alignment
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from Bio.Align import MultipleSeqAlignment
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from Bio.Restriction import AluI
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from Bio.Restriction import EcoRI
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from Bio.Seq import Seq
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from Bio.SeqRecord import SeqRecord
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def createAlignment(sequences):
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"""Create an Alignment object from a list of sequences."""
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return Alignment(
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[
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SeqRecord(Seq(s), id="sequence%i" % (i + 1))
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for (i, s) in enumerate(sequences)
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]
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)
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def createMultipleSeqAlignment(sequences):
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"""Create a MultipleSeqAlignment object from a list of sequences."""
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return MultipleSeqAlignment(
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SeqRecord(Seq(s), id="sequence%i" % (i + 1)) for (i, s) in enumerate(sequences)
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)
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class TestCAPS(unittest.TestCase):
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def test_trivial(self):
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enzymes = [EcoRI]
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alignment = ["gaattc", "gaactc"]
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align = createAlignment(alignment)
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capsmap = CAPS.CAPSMap(align, enzymes)
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self.assertEqual(len(capsmap.dcuts), 1)
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self.assertEqual(capsmap.dcuts[0].enzyme, EcoRI)
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self.assertEqual(capsmap.dcuts[0].start, 1)
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self.assertEqual(capsmap.dcuts[0].cuts_in, [0])
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self.assertEqual(capsmap.dcuts[0].blocked_in, [1])
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def test_trivial_msa(self):
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enzymes = [EcoRI]
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alignment = ["gaattc", "gaactc"]
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align = createMultipleSeqAlignment(alignment)
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capsmap = CAPS.CAPSMap(align, enzymes)
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self.assertEqual(len(capsmap.dcuts), 1)
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self.assertEqual(capsmap.dcuts[0].enzyme, EcoRI)
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self.assertEqual(capsmap.dcuts[0].start, 1)
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self.assertEqual(capsmap.dcuts[0].cuts_in, [0])
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self.assertEqual(capsmap.dcuts[0].blocked_in, [1])
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def test(self):
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alignment = [
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"AAAagaattcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
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"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
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"TTAGTGAAAATGGAGGATCAAGTagAtTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
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"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
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"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
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"AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
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"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
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"TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
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"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
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"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
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"AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
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"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
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"TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
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"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
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"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
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]
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self.assertEqual(len(alignment), 3)
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enzymes = [EcoRI, AluI]
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align = createAlignment(alignment)
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capsmap = CAPS.CAPSMap(align, enzymes)
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self.assertEqual(len(capsmap.dcuts), 2)
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self.assertEqual(capsmap.dcuts[0].enzyme, EcoRI)
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self.assertEqual(capsmap.dcuts[0].start, 5)
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self.assertEqual(capsmap.dcuts[0].cuts_in, [0])
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self.assertEqual(capsmap.dcuts[0].blocked_in, [1, 2])
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self.assertEqual(capsmap.dcuts[1].enzyme, AluI)
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self.assertEqual(capsmap.dcuts[1].start, 144)
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self.assertEqual(capsmap.dcuts[1].cuts_in, [1, 2])
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self.assertEqual(capsmap.dcuts[1].blocked_in, [0])
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def test_msa(self):
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alignment = [
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"AAAagaattcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
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"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
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"TTAGTGAAAATGGAGGATCAAGTagAtTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
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"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
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"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
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"AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
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"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
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"TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
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"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
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"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
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"AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT"
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"AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT"
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"TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT"
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"GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC"
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"AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC",
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]
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self.assertEqual(len(alignment), 3)
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enzymes = [EcoRI, AluI]
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align = createMultipleSeqAlignment(alignment)
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capsmap = CAPS.CAPSMap(align, enzymes)
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self.assertEqual(len(capsmap.dcuts), 2)
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self.assertEqual(capsmap.dcuts[0].enzyme, EcoRI)
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self.assertEqual(capsmap.dcuts[0].start, 5)
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self.assertEqual(capsmap.dcuts[0].cuts_in, [0])
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self.assertEqual(capsmap.dcuts[0].blocked_in, [1, 2])
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self.assertEqual(capsmap.dcuts[1].enzyme, AluI)
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self.assertEqual(capsmap.dcuts[1].start, 144)
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self.assertEqual(capsmap.dcuts[1].cuts_in, [1, 2])
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self.assertEqual(capsmap.dcuts[1].blocked_in, [0])
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def testNoCAPS(self):
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alignment = ["aaaaaaaaaaaaaaaaaaaa", "aaaaaaaaaaaaaaaaaaaa"]
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enzymes = []
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align = createAlignment(alignment)
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capsmap = CAPS.CAPSMap(align, enzymes)
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self.assertEqual(capsmap.dcuts, [])
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def testNoCAPS_msa(self):
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alignment = ["aaaaaaaaaaaaaaaaaaaa", "aaaaaaaaaaaaaaaaaaaa"]
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enzymes = []
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align = createMultipleSeqAlignment(alignment)
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capsmap = CAPS.CAPSMap(align, enzymes)
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self.assertEqual(capsmap.dcuts, [])
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def test_uneven(self):
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alignment = [
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"aaaaaaaaaaaaaa",
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"aaaaaaaaaaaaaa", # we'll change this below
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"aaaaaaaaaaaaaa",
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]
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align = createMultipleSeqAlignment(alignment)
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align[1].seq = align[1].seq[:8] # evil
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self.assertRaises(CAPS.AlignmentHasDifferentLengthsError, CAPS.CAPSMap, align)
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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