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biopython/Tests/test_SearchIO_exonerate.py
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  --config=lint.isort.order-by-type=false \
  BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py

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# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for SearchIO ExonerateIO parsers."""
import os
import unittest
from Bio.SearchIO import parse
from Bio.SearchIO import read
# test case files are in the Blast directory
TEST_DIR = "Exonerate"
def get_file(filename):
"""Return the path of a test file."""
return os.path.join(TEST_DIR, filename)
class ExonerateSpcCases(unittest.TestCase):
coord = ("start", "end")
coords = ("inter_ranges",)
stype = ("hit_", "query_")
def check_vulgar_text(self, vulgar, text):
"""Compare coordinate parsing for vulgar and text formats."""
vfile = get_file(vulgar)
tfile = get_file(text)
vqres = read(vfile, "exonerate-vulgar")
tqres = read(tfile, "exonerate-text")
# compare coordinates of vulgar and text formats
# should be the same since the files are results of the same query
# vs db search
for vhit, thit in zip(vqres, tqres):
for vhsp, thsp in zip(vhit.hsps, thit.hsps):
self.assertEqual(vhsp.query_start, thsp.query_start)
self.assertEqual(vhsp.hit_start, thsp.hit_start)
self.assertEqual(vhsp.query_end, thsp.query_end)
self.assertEqual(vhsp.hit_end, thsp.hit_end)
self.assertEqual(vhsp.query_inter_ranges, thsp.query_inter_ranges)
self.assertEqual(vhsp.hit_inter_ranges, thsp.hit_inter_ranges)
self.assertEqual(vhsp.query_split_codons, thsp.query_split_codons)
self.assertEqual(vhsp.hit_split_codons, thsp.hit_split_codons)
self.assertEqual(vhsp.query_frame_all, thsp.query_frame_all)
self.assertEqual(vhsp.hit_frame_all, thsp.hit_frame_all)
def test_vulgar_text_similar_g2g(self):
"""Compares vulgar-text coordinate parsing for the genome2genome model."""
self.check_vulgar_text("exn_22_o_vulgar.exn", "exn_22_m_genome2genome.exn")
def test_vulgar_text_similar_c2c(self):
"""Compares vulgar-text coordinate parsing for the coding2coding model."""
self.check_vulgar_text(
"exn_22_o_vulgar_fshifts.exn", "exn_22_m_coding2coding_fshifts.exn"
)
def test_vulgar_text_similar_p2d(self):
"""Compares vulgar-text coordinate parsing for the protein2dna model."""
self.check_vulgar_text(
"exn_22_o_vulgar_fshifts2.exn", "exn_22_m_protein2dna_fshifts.exn"
)
class ExonerateTextCases(unittest.TestCase):
fmt = "exonerate-text"
def test_exn_22_m_affine_local(self):
"""Test parsing exonerate output (exn_22_m_affine_local.exn)."""
exn_file = get_file("exn_22_m_affine_local.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("affine:local:dna2dna", qresult.model)
self.assertEqual(3, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(6150, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443688|ref|NC_001145.3|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XIII, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(359, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(83, hsp.query_start)
self.assertEqual(253990, hsp.hit_start)
self.assertEqual(552, hsp.query_end)
self.assertEqual(254474, hsp.hit_end)
self.assertEqual([(83, 552)], hsp.query_range_all)
self.assertEqual([(253990, 254474)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ACCTAAGAGGAAGGTGGGCAGACCAGGCAGAAAA-AGGAT", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||| |||| ||||| ||| | | ||| ||| | |||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACCGAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGAT", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"AAGTTATGTGGAACA--TAGGCTCATGGAACGCTCCCAGT", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"| || | | |||| || ||| || | ||| |||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"ATGT--GGGGAAACAATTACCTTCACCAAATGATCCAAGT", hsp.hit_all[0].seq[-40:]
)
# third hit
hit = qresult[2]
self.assertEqual("gi|330443715|ref|NC_001146.8|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XIV, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# third hit, first hsp
hsp = qresult[2].hsps[0]
self.assertEqual(219, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(60, hsp.query_start)
self.assertEqual(454073, hsp.hit_start)
self.assertEqual(517, hsp.query_end)
self.assertEqual(454531, hsp.hit_end)
self.assertEqual([(60, 517)], hsp.query_range_all)
self.assertEqual([(454073, 454531)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTG-", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||| || || || | ||||| | |||| || | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGATGATATATTA-GATGGGG-ATG-AAGATGAGCCAGA", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"G-TATAGAAGTACAGCCGCACACTCAAGAGAATGAGAAAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"| | ||||| | | | | | | ||| | |||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GTTGAAGAAGCCAAACGGAAGAAAGACGAGGA-GAGAAAG", hsp.hit_all[0].seq[-40:]
)
def test_exn_22_m_cdna2genome(self):
"""Test parsing exonerate output (exn_22_m_cdna2genome.exn)."""
exn_file = get_file("exn_22_m_cdna2genome.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("cdna2genome", qresult.model)
self.assertEqual(2, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(2, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(6146, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# first hit, second hsp
hsp = qresult[0].hsps[1]
self.assertEqual(6146, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGA", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGA", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"CTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT", hsp.hit_all[0].seq[-40:]
)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443688|ref|NC_001145.3|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XIII, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(518, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(85010, hsp.hit_start)
self.assertEqual(516, hsp.query_end)
self.assertEqual(667216, hsp.hit_end)
self.assertEqual(
[(0, 65), (65, 225), (225, 320), (320, 346), (346, 516)],
hsp.query_range_all,
)
self.assertEqual(
[
(85010, 85066),
(253974, 254135),
(350959, 351052),
(473170, 473201),
(667040, 667216),
],
hsp.hit_range_all,
)
self.assertEqual(
[(65, 65), (225, 225), (320, 320), (346, 346)], hsp.query_inter_ranges
)
self.assertEqual(
[(85066, 253974), (254135, 350959), (351052, 473170), (473201, 667040)],
hsp.hit_inter_ranges,
)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(5, len(hsp.query_all))
self.assertEqual(5, len(hsp.hit_all))
# first block
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"|||| || | |||| | |||||| |||| | | | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGTGAACCT-CTTCAAGACGGTCAG--AATA-A-TCAA", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"AGCAAATATATTTAGCAGGTGACATGAAGAAGCAAATGTT", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"|| |||| | | | |||| ||||||||||||| | |",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"AG--AATA-A-TCAACAGG----ATGAAGAAGCAAAAGAT", hsp.hit_all[0].seq[-40:]
)
# last block
self.assertEqual(
"TATTAGCCTTCC--TCGATGATCTGCA--A-GAACAACAG", hsp.query_all[-1].seq[:40]
)
self.assertEqual(
"| |||| || | ||||| | || || | ||| | | ",
hsp[-1].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TCATAGCGTTACGTTCGAT-ACCTTCACTACGAAGATCCA", hsp.hit_all[-1].seq[:40]
)
self.assertEqual(
"AAGTATAGAAGTACAGCCGCACACTCAAGAGAATGAGAAA", hsp.query_all[-1].seq[-40:]
)
self.assertEqual(
" ||||||||||||| || ||| | || | |||",
hsp[-1].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TTCTATAGAAGTACAGTTATTCAAACAAAAAAAAAAAAAA", hsp.hit_all[-1].seq[-40:]
)
def test_exn_22_m_coding2coding(self):
"""Test parsing exonerate output (exn_22_m_coding2coding.exn)."""
exn_file = get_file("exn_22_m_coding2coding.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("coding2coding", qresult.model)
self.assertEqual(2, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(2, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(2151, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(1, hsp.query_start)
self.assertEqual(1318047, hsp.hit_start)
self.assertEqual(1228, hsp.query_end)
self.assertEqual(1319274, hsp.hit_end)
self.assertEqual([(1, 1228)], hsp.query_range_all)
self.assertEqual([(1318047, 1319274)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGC", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGC", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", hsp.hit_all[0].seq[-40:]
)
# first hit, second hsp
hsp = qresult[0].hsps[1]
self.assertEqual(2106, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443688|ref|NC_001145.3|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XIII, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(116, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(1065, hsp.query_start)
self.assertEqual(255638, hsp.hit_start)
self.assertEqual(1224, hsp.query_end)
self.assertEqual(255794, hsp.hit_end)
self.assertEqual([(1065, 1224)], hsp.query_range_all)
self.assertEqual([(255638, 255794)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"TGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAAT", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||+! .!.||| !!:...||+:!::!:! ||+||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TGTTCGGAAATTTGGGATAGAATAACAACACATCCGAAAT", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"CAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTC", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"!!!.||+...|||:!:||+ |||+|| !!::!!.:!:",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CAATGCAGAAGACGTTCAATTAGCTTTGAATAAGCATATG", hsp.hit_all[0].seq[-40:]
)
def test_exn_22_m_coding2genome(self):
"""Test parsing exonerate output (exn_22_m_coding2genome.exn)."""
exn_file = get_file("exn_22_m_coding2genome.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("coding2genome", qresult.model)
self.assertEqual(2, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(2, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(2151, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(1, hsp.query_start)
self.assertEqual(1318047, hsp.hit_start)
self.assertEqual(1228, hsp.query_end)
self.assertEqual(1319274, hsp.hit_end)
self.assertEqual([(1, 1228)], hsp.query_range_all)
self.assertEqual([(1318047, 1319274)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGC", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGC", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", hsp.hit_all[0].seq[-40:]
)
# first hit, second hsp
hsp = qresult[0].hsps[1]
self.assertEqual(2106, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443688|ref|NC_001145.3|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XIII, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(116, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(1065, hsp.query_start)
self.assertEqual(255638, hsp.hit_start)
self.assertEqual(1224, hsp.query_end)
self.assertEqual(255794, hsp.hit_end)
self.assertEqual([(1065, 1224)], hsp.query_range_all)
self.assertEqual([(255638, 255794)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"TGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAAT", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||+! .!.||| !!:...||+:!::!:! ||+||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TGTTCGGAAATTTGGGATAGAATAACAACACATCCGAAAT", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"CAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTC", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"!!!.||+...|||:!:||+ |||+|| !!::!!.:!:",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CAATGCAGAAGACGTTCAATTAGCTTTGAATAAGCATATG", hsp.hit_all[0].seq[-40:]
)
def test_exn_22_m_dna2protein(self):
"""Test parsing exonerate output (exn_22_m_dna2protein.exn)."""
exn_file = get_file("exn_22_m_dna2protein.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("dna", qresult.id)
self.assertEqual("", qresult.description)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("ungapped:dna2protein", qresult.model)
self.assertEqual(1, len(qresult))
hit = qresult[0]
self.assertEqual("protein", hit.id)
self.assertEqual("", hit.description)
self.assertEqual(1, len(hit.hsps))
hsp = hit[0]
self.assertEqual(105, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(0, hsp[0].hit_strand)
self.assertEqual(0, hsp[0].query_start)
self.assertEqual(93, hsp[0].query_end)
self.assertEqual(313, hsp[0].hit_start)
self.assertEqual(344, hsp[0].hit_end)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual("NSPFXKGPLASVQNPVYHKQPLNPAPNAETH", hsp[0].query.seq[:40])
self.assertEqual(
["|||", "...", " !!", " !!", "! !"], hsp[0].aln_annotation["similarity"][:5]
)
self.assertEqual("NQSVPKRPAGSVQNPVYHNQPLNPAPSRDPH", hsp[0].hit.seq[:40])
def test_exn_22_m_est2genome(self):
"""Test parsing exonerate output (exn_22_m_est2genome.exn)."""
exn_file = get_file("exn_22_m_est2genome.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("est2genome", qresult.model)
self.assertEqual(2, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(6150, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443688|ref|NC_001145.3|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XIII, complete sequence",
hit.description,
)
self.assertEqual(2, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(439, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(85010, hsp.hit_start)
self.assertEqual(346, hsp.query_end)
self.assertEqual(473201, hsp.hit_end)
self.assertEqual(
[(0, 65), (65, 225), (225, 320), (320, 346)], hsp.query_range_all
)
self.assertEqual(
[(85010, 85066), (253974, 254135), (350959, 351052), (473170, 473201)],
hsp.hit_range_all,
)
self.assertEqual([(65, 65), (225, 225), (320, 320)], hsp.query_inter_ranges)
self.assertEqual(
[(85066, 253974), (254135, 350959), (351052, 473170)], hsp.hit_inter_ranges
)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(4, len(hsp.query_all))
self.assertEqual(4, len(hsp.hit_all))
# first block
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"|||| || | |||| | |||||| |||| | | | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGTGAACCT-CTTCAAGACGGTCAG--AATA-A-TCAA", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"AGCAAATATATTTAGCAGGTGACATGAAGAAGCAAATGTT", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"|| |||| | | | |||| ||||||||||||| | |",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"AG--AATA-A-TCAACAGG----ATGAAGAAGCAAAAGAT", hsp.hit_all[0].seq[-40:]
)
# last block
self.assertEqual("AGCTAAGAATTCTGATGATG-----AAAGAA", hsp.query_all[-1].seq)
self.assertEqual(
"| |||||||||||| ||| ||||||", hsp[-1].aln_annotation["similarity"]
)
self.assertEqual("ATGGAAGAATTCTGATAATGCTGTAAAAGAA", hsp.hit_all[-1].seq)
# second hit, second hsp
hsp = qresult[1].hsps[1]
self.assertEqual(263, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(25, hsp.query_start)
self.assertEqual(11338, hsp.hit_start)
self.assertEqual(406, hsp.query_end)
self.assertEqual(130198, hsp.hit_end)
self.assertEqual([(25, 183), (183, 252), (252, 406)], hsp.query_range_all)
self.assertEqual(
[(130038, 130198), (120612, 120681), (11338, 11487)], hsp.hit_range_all
)
self.assertEqual([(183, 183), (252, 252)], hsp.query_inter_ranges)
self.assertEqual([(120681, 130038), (11487, 120612)], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(3, len(hsp.query_all))
self.assertEqual(3, len(hsp.hit_all))
# first block
self.assertEqual(
"AGCAAATATATTTA-GCAGGTGACATGAAGAAGCAAATGT", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"| |||| ||| | |||| | | || |||| | | |",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACCAAAGATAACAAGGCAG--AAAAAGAGGAAGAAGAAAT", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"AG-GACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"|| ||| |||||| || ||| || || ||| ||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"AGTGAC--CCCAGAGGAGCCAAGCAAAAAGA---TTCGGA", hsp.hit_all[0].seq[-40:]
)
# last block
self.assertEqual(
"AATAAGACTACCACGGACTTTTTACTATGTTCTTTAAAAA", hsp.query_all[-1].seq[:40]
)
self.assertEqual(
"||||||| | ||| | |||| | | | | || ",
hsp[-1].aln_annotation["similarity"][:40],
)
self.assertEqual(
"AATAAGAGCAACACAG----TTTA-TCTTATATGTA----", hsp.hit_all[-1].seq[:40]
)
self.assertEqual(
"CTGCAAGAACAACAGAAAAGGGAAAACGAAAAAGGAACAA", hsp.query_all[-1].seq[-40:]
)
self.assertEqual(
"| | | || | | || || |||||||| || ||||",
hsp[-1].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CCACTAAAAAATTATAAGAGCCAAAACGAAGTAGATACAA", hsp.hit_all[-1].seq[-40:]
)
def test_exn_22_m_genome2genome(self):
"""Test parsing exonerate output (exn_22_m_genome2genome.exn)."""
exn_file = get_file("exn_22_m_genome2genome.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("sacCer3_dna", qresult.id)
self.assertEqual(
"range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("genome2genome", qresult.model)
self.assertEqual(3, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(2, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(2641, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1319468, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(1319997, hsp.hit_end)
self.assertEqual([(0, 529)], hsp.query_range_all)
self.assertEqual([(1319468, 1319997)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATCCCTTATCTCTTTATCTTGTTGCCTGGTTCTCTTTTCC", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATCCCTTATCTCTTTATCTTGTTGCCTGGTTCTCTTTTCC", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"ACGGCAATACCTGGCATGTGATTGTCGGAAAGAACTTTGG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"ACGGCAATACCTGGCATGTGATTGTCGGAAAGAACTTTGG", hsp.hit_all[0].seq[-40:]
)
# first hit, second hsp
hsp = qresult[0].hsps[1]
self.assertEqual(2641, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1319468, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(1319997, hsp.hit_end)
self.assertEqual([(0, 529)], hsp.query_range_all)
self.assertEqual([(1319468, 1319997)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"CCAAAGTTCTTTCCGACAATCACATGCCAGGTATTGCCGT", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"CCAAAGTTCTTTCCGACAATCACATGCCAGGTATTGCCGT", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"GGAAAAGAGAACCAGGCAACAAGATAAAGAGATAAGGGAT", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GGAAAAGAGAACCAGGCAACAAGATAAAGAGATAAGGGAT", hsp.hit_all[0].seq[-40:]
)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443489|ref|NC_001135.5|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome III, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(267, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(162, hsp.query_start)
self.assertEqual(23668, hsp.hit_start)
self.assertEqual(491, hsp.query_end)
self.assertEqual(115569, hsp.hit_end)
self.assertEqual(
[(462, 491), (413, 462), (378, 413), (302, 378), (162, 302)],
hsp.query_range_all,
)
self.assertEqual(
[
(23668, 23697),
(32680, 32732),
(42287, 42325),
(97748, 97821),
(115419, 115569),
],
hsp.hit_range_all,
)
self.assertEqual(
[(462, 462), (413, 413), (378, 378), (302, 302)], hsp.query_inter_ranges
)
self.assertEqual(
[(23697, 32680), (32732, 42287), (42325, 97748), (97821, 115419)],
hsp.hit_inter_ranges,
)
self.assertEqual([(378, 379), (376, 378)], hsp.query_split_codons)
self.assertEqual([(42324, 42325), (97748, 97750)], hsp.hit_split_codons)
self.assertEqual(5, len(hsp.query_all))
self.assertEqual(5, len(hsp.hit_all))
# first block
self.assertEqual("CCCTTTAAATGGAGATTACAAACTAGCGA", hsp.query_all[0].seq)
self.assertEqual(
"|| | ||| | ||| ||||| | | |", hsp[0].aln_annotation["similarity"]
)
self.assertEqual("CCGCTGAAAGGAAGAGAACAAAGTTACAA", hsp.hit_all[0].seq)
# last block
self.assertEqual(
"TTTTCTTTACTAAC-TCGAGGAAGAGTGAGGTTTTCTTCC", hsp.query_all[-1].seq[:40]
)
self.assertEqual(
"| || || | | | |||||| |||| | | | |||",
hsp[-1].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TCTTGAAGACCAGCATGTAGGAAG-GTGATGATATGCTCC", hsp.hit_all[-1].seq[:40]
)
self.assertEqual(
"TTTGTGTGTGTACATTTGAATATATATATTTAC-TAACAA", hsp.query_all[-1].seq[-40:]
)
self.assertEqual(
" ||| ||| | ||||||||||||| | | ||||||",
hsp[-1].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"ATTGATTGTTTTGTTTTGAATATATATTGATGCTTAACAA", hsp.hit_all[-1].seq[-40:]
)
# third hit
hit = qresult[2]
self.assertEqual("gi|330443667|ref|NC_001143.9|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XI, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# third hit, first hsp
hsp = qresult[2].hsps[0]
self.assertEqual(267, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(78, hsp.query_start)
self.assertEqual(71883, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(641760, hsp.hit_end)
self.assertEqual(
[(449, 529), (319, 388), (198, 284), (161, 198), (78, 114)],
hsp.query_range_all,
)
self.assertEqual(
[
(641682, 641760),
(487327, 487387),
(386123, 386207),
(208639, 208677),
(71883, 71917),
],
hsp.hit_range_all,
)
self.assertEqual(
[(388, 449), (284, 319), (198, 198), (114, 161)], hsp.query_inter_ranges
)
self.assertEqual(
[(487387, 641682), (386207, 487327), (208677, 386123), (71917, 208639)],
hsp.hit_inter_ranges,
)
self.assertEqual([(198, 200), (197, 198)], hsp.query_split_codons)
self.assertEqual([(386123, 386125), (208676, 208677)], hsp.hit_split_codons)
self.assertEqual(5, len(hsp.query_all))
self.assertEqual(5, len(hsp.hit_all))
# first block
self.assertEqual(
"ATCCCTTATCTCTTTATCTTGTTGCCTGGTTCTCTTTTCC", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"|||||||||||||| ||| ||||| |||| ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATCCCTTATCTCTTCTAAAGATTGTGTGGTT---TTTT--", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"AAATGGAGATTACAA---ACTAGCGAA-ACTGCAGAAAAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
" || || ||| || || || || || | |||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GCATATTTTTTCCAACCTTCTTGCCAATTCTTCA-ACAAG", hsp.hit_all[0].seq[-40:]
)
# last block
self.assertEqual("TAAAGATGCTCTGGACAAGTACCAGTTGGAAAGAGA", hsp.query_all[-1].seq)
self.assertEqual(
" |||||| ||| || | | ||||||||||||||", hsp[-1].aln_annotation["similarity"]
)
self.assertEqual("AAAAGATTTTCT--ACGACTTGCAGTTGGAAAGAGA", hsp.hit_all[-1].seq)
def test_exn_22_m_ungapped(self):
"""Test parsing exonerate output (exn_22_m_ungapped.exn)."""
exn_file = get_file("exn_22_m_ungapped.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("ungapped:dna2dna", qresult.model)
self.assertEqual(2, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(6150, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443688|ref|NC_001145.3|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XIII, complete sequence",
hit.description,
)
self.assertEqual(2, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(233, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(121, hsp.query_start)
self.assertEqual(254031, hsp.hit_start)
self.assertEqual(236, hsp.query_end)
self.assertEqual(254146, hsp.hit_end)
self.assertEqual([(121, 236)], hsp.query_range_all)
self.assertEqual([(254031, 254146)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"TTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"| || ||||| ||||| | |||||||||||| ||| |",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TGGATCCTGAAACTAAGCAGAAGAGGACTGCCCAAAATCG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"CCAAAATGAAGAGTTTGCAAGAGAGGGTAGAGTTACTAGA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
" || |||||| ||| | ||| |||| | ||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GGAAGATGAAGGAATTGGAGAAGAAGGTACAAAGTTTAGA", hsp.hit_all[0].seq[-40:]
)
# second hit, second hsp
hsp = qresult[1].hsps[1]
self.assertEqual(151, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(1098, hsp.query_start)
self.assertEqual(255671, hsp.hit_start)
self.assertEqual(1166, hsp.query_end)
self.assertEqual(255739, hsp.hit_end)
self.assertEqual([(1098, 1166)], hsp.query_range_all)
self.assertEqual([(255671, 255739)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"CCAAAATATTCATCGTTGGACATAGATGATTTATGCAGCG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"|| ||||| ||| | || | |||| |||||| ||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"CCGAAATACTCAGATATTGATGTCGATGGTTTATGTTCCG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"ATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
" |||||| ||| |||| |||||||||||| ||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GTTTATGTTCCGAGCTAATGGCAAAGGCAAAATGTTCAGA", hsp.hit_all[0].seq[-40:]
)
def test_exn_22_m_ungapped_trans(self):
"""Test parsing exonerate output (exn_22_m_ungapped_trans.exn)."""
exn_file = get_file("exn_22_m_ungapped_trans.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("ungapped:codon", qresult.model)
self.assertEqual(1, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(3, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(2151, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(1, hsp.query_start)
self.assertEqual(1318047, hsp.hit_start)
self.assertEqual(1228, hsp.query_end)
self.assertEqual(1319274, hsp.hit_end)
self.assertEqual([(1, 1228)], hsp.query_range_all)
self.assertEqual([(1318047, 1319274)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGC", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGC", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", hsp.hit_all[0].seq[-40:]
)
# first hit, second hsp
hsp = qresult[0].hsps[1]
self.assertEqual(2106, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# first hit, third hsp
hsp = qresult[0].hsps[2]
self.assertEqual(2072, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGA", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGA", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"CTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT", hsp.hit_all[0].seq[-40:]
)
def test_exn_22_m_ner(self):
"""Test parsing exonerate output (exn_22_m_ner.exn)."""
exn_file = get_file("exn_22_m_ner.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("NER:affine:local:dna2dna", qresult.model)
self.assertEqual(2, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(2, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(6150, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all[:5])
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all[:5])
self.assertEqual([], hsp.query_inter_ranges[:5])
self.assertEqual([], hsp.hit_inter_ranges[:5])
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# first hit, second hsp
hsp = qresult[0].hsps[1]
self.assertEqual(440, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(509, hsp.query_start)
self.assertEqual(183946, hsp.hit_start)
self.assertEqual(1192, hsp.query_end)
self.assertEqual(184603, hsp.hit_end)
self.assertEqual(
[(509, 514), (537, 547), (567, 595), (607, 617), (636, 650)],
hsp.query_range_all[:5],
)
self.assertEqual(
[
(183946, 183951),
(183977, 183987),
(184002, 184030),
(184044, 184054),
(184066, 184080),
],
hsp.hit_range_all[:5],
)
self.assertEqual(
[(514, 537), (547, 567), (595, 607), (617, 636), (650, 667)],
hsp.query_inter_ranges[:5],
)
self.assertEqual(
[
(183951, 183977),
(183987, 184002),
(184030, 184044),
(184054, 184066),
(184080, 184092),
],
hsp.hit_inter_ranges[:5],
)
self.assertEqual(24, len(hsp.query_all))
self.assertEqual(24, len(hsp.hit_all))
# first block
self.assertEqual("TGAGA", hsp.query_all[0].seq)
self.assertEqual("|||||", hsp[0].aln_annotation["similarity"])
self.assertEqual("TGAGA", hsp.hit_all[0].seq)
# last block
self.assertEqual("GACTGCAAAATAGTAGTCAAAGCTC", hsp.query_all[-1].seq)
self.assertEqual(
"||| | ||||||||||||| | |||", hsp[-1].aln_annotation["similarity"]
)
self.assertEqual("GACGGTAAAATAGTAGTCACACCTC", hsp.hit_all[-1].seq)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443681|ref|NC_001144.5|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome XII, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(502, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(110, hsp.query_start)
self.assertEqual(297910, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(318994, hsp.hit_end)
self.assertEqual(
[(110, 117), (148, 159), (169, 182), (184, 197), (227, 244)],
hsp.query_range_all[:5],
)
self.assertEqual(
[
(297910, 297917),
(297946, 297957),
(297970, 297983),
(297992, 298004),
(298019, 298038),
],
hsp.hit_range_all[:5],
)
self.assertEqual(
[(117, 148), (159, 169), (182, 184), (197, 227), (244, 255)],
hsp.query_inter_ranges[:5],
)
self.assertEqual(
[
(297917, 297946),
(297957, 297970),
(297983, 297992),
(298004, 298019),
(298038, 298049),
],
hsp.hit_inter_ranges[:5],
)
self.assertEqual(33, len(hsp.query_all))
self.assertEqual(33, len(hsp.hit_all))
# first block
self.assertEqual("CAGAAAA", hsp.query_all[0].seq)
self.assertEqual("| |||||", hsp[0].aln_annotation["similarity"])
self.assertEqual("CTGAAAA", hsp.hit_all[0].seq)
# last block
self.assertEqual("TGGTTAGACAGCTCCTGTAG", hsp.query_all[-1].seq)
self.assertEqual("|| | ||||||||||||||", hsp[-1].aln_annotation["similarity"])
self.assertEqual("TGATAGGACAGCTCCTGTAG", hsp.hit_all[-1].seq)
def test_exn_22_q_multiple(self):
"""Test parsing exonerate output (exn_22_q_multiple.exn)."""
exn_file = get_file("exn_22_q_multiple.exn")
qresults = list(parse(exn_file, self.fmt))
self.assertEqual(2, len(qresults))
# check common attributes
for qresult in qresults:
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
# test first qresult
qresult = qresults[0]
self.assertEqual("gi|296142823|ref|NM_001178508.1|", qresult.id)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("est2genome", qresult.model)
self.assertEqual(3, len(qresult))
# first qresult, first hit
hit = qresult[0]
self.assertEqual("gi|330443482|ref|NC_001134.8|", hit.id)
self.assertEqual(1, len(hit.hsps))
# first qresult, first hit, first hsp
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(4485, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(560077, hsp.hit_start)
self.assertEqual(897, hsp.query_end)
self.assertEqual(560974, hsp.hit_end)
self.assertEqual([(0, 897)], hsp.query_range_all)
self.assertEqual([(560077, 560974)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGAGCGGTGAATTAGCAAATTACAAAAGACTTGAGAAAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGAGCGGTGAATTAGCAAATTACAAAAGACTTGAGAAAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"CAGAAGAGCAGCCATCCACCCCTACTTCCAAGAATCATAA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CAGAAGAGCAGCCATCCACCCCTACTTCCAAGAATCATAA", hsp.hit_all[0].seq[-40:]
)
# first qresult, second hit
hit = qresult[1]
self.assertEqual("gi|330443753|ref|NC_001148.4|", hit.id)
self.assertEqual(1, len(hit.hsps))
# first qresult, second hit, first hsp
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(941, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(2, hsp.query_start)
self.assertEqual(492033, hsp.hit_start)
self.assertEqual(896, hsp.query_end)
self.assertEqual(492933, hsp.hit_end)
self.assertEqual([(2, 896)], hsp.query_range_all)
self.assertEqual([(492033, 492933)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"GAGCGGTGAATTAGCAAATTACAAAAGACTTGAGAAAGTC", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"|||| | || | || ||| | || | || || | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"GAGC--TCTATGAACAGATTTAAGCAG-TTAGAAAAGCTT", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"C-AGAAGAGCAGCCATCCACCCCTACTTCCAAGAATCATA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"| || || ||| ||||| | || ||| | ||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CAAGCAGGCTCTGCAT-CACCCTTGGTTTGCAGAGTACTA", hsp.hit_all[0].seq[-40:]
)
# first qresult, third hit
hit = qresult[2]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(1, len(hit.hsps))
# first qresult, third hit, first hsp
# third hit, first hsp
hsp = qresult[2].hsps[0]
self.assertEqual(651, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(34, hsp.query_start)
self.assertEqual(267809, hsp.hit_start)
self.assertEqual(721, hsp.query_end)
self.assertEqual(300717, hsp.hit_end)
self.assertEqual([(34, 691), (691, 721)], hsp.query_range_all)
self.assertEqual([(267809, 268448), (300686, 300717)], hsp.hit_range_all)
self.assertEqual([(691, 691)], hsp.query_inter_ranges)
self.assertEqual([(268448, 300686)], hsp.hit_inter_ranges)
self.assertEqual(2, len(hsp.query_all))
self.assertEqual(2, len(hsp.hit_all))
# first block
self.assertEqual(
"AGAAAGTCGGTGAAGGTACATACGGTGTTGTTTATAAAGC", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||| ||||| ||||| || | |||||||| | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"AGAAAGTTGGTGAGGGTACTTATGCGGTTGTTTA-CTTGG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"CGATCAGATTTTCAAG--ATATTCAGAGTATTGGGAACGC", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"|||||| | | ||| | ||||| | || || || |",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CGATCAAA--TGGAAGTAACGTTCAGGGCCTTAGGGACAC", hsp.hit_all[0].seq[-40:]
)
# last block
self.assertEqual("CGAATGAAGCTA-TATGGCCAGATATTGTCT", hsp.query_all[-1].seq)
self.assertEqual(
"| || || || ||||||||||||| |||", hsp[-1].aln_annotation["similarity"]
)
self.assertEqual("CAAACCGAGATAGAATGGCCAGATATTCTCT", hsp.hit_all[-1].seq)
# test second qresult
qresult = qresults[1]
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("est2genome", qresult.model)
self.assertEqual(2, len(qresult))
# second qresult, first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(1, len(hit.hsps))
# second qresult, first hit, first hsp
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(6150, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318045, hsp.hit_start)
self.assertEqual(1230, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual([(0, 1230)], hsp.query_range_all)
self.assertEqual([(1318045, 1319275)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", hsp.hit_all[0].seq[-40:]
)
# second qresult, second hit
hit = qresult[1]
self.assertEqual("gi|330443688|ref|NC_001145.3|", hit.id)
self.assertEqual(2, len(hit.hsps))
# second qresult, second hit, first hsp
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(439, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(85010, hsp.hit_start)
self.assertEqual(346, hsp.query_end)
self.assertEqual(473201, hsp.hit_end)
self.assertEqual(
[(0, 65), (65, 225), (225, 320), (320, 346)], hsp.query_range_all
)
self.assertEqual(
[(85010, 85066), (253974, 254135), (350959, 351052), (473170, 473201)],
hsp.hit_range_all,
)
self.assertEqual([(65, 65), (225, 225), (320, 320)], hsp.query_inter_ranges)
self.assertEqual(
[(85066, 253974), (254135, 350959), (351052, 473170)], hsp.hit_inter_ranges
)
self.assertEqual(4, len(hsp.query_all))
self.assertEqual(4, len(hsp.hit_all))
# first block
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"|||| || | |||| | |||||| |||| | | | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGTGAACCT-CTTCAAGACGGTCAG--AATA-A-TCAA", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"AGCAAATATATTTAGCAGGTGACATGAAGAAGCAAATGTT", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"|| |||| | | | |||| ||||||||||||| | |",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"AG--AATA-A-TCAACAGG----ATGAAGAAGCAAAAGAT", hsp.hit_all[0].seq[-40:]
)
# last block
self.assertEqual("AGCTAAGAATTCTGATGATG-----AAAGAA", hsp.query_all[-1].seq)
self.assertEqual(
"| |||||||||||| ||| ||||||", hsp[-1].aln_annotation["similarity"]
)
self.assertEqual("ATGGAAGAATTCTGATAATGCTGTAAAAGAA", hsp.hit_all[-1].seq)
# second qresult, second hit, second hsp
# second hit, second hsp
hsp = qresult[1].hsps[1]
self.assertEqual(263, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(25, hsp.query_start)
self.assertEqual(11338, hsp.hit_start)
self.assertEqual(406, hsp.query_end)
self.assertEqual(130198, hsp.hit_end)
self.assertEqual([(25, 183), (183, 252), (252, 406)], hsp.query_range_all)
self.assertEqual(
[(130038, 130198), (120612, 120681), (11338, 11487)], hsp.hit_range_all
)
self.assertEqual([(183, 183), (252, 252)], hsp.query_inter_ranges)
self.assertEqual([(120681, 130038), (11487, 120612)], hsp.hit_inter_ranges)
self.assertEqual(3, len(hsp.query_all))
self.assertEqual(3, len(hsp.hit_all))
# first block
self.assertEqual(
"AGCAAATATATTTA-GCAGGTGACATGAAGAAGCAAATGT", hsp.query_all[0].seq[:40]
)
self.assertEqual(
"| |||| ||| | |||| | | || |||| | | |",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACCAAAGATAACAAGGCAG--AAAAAGAGGAAGAAGAAAT", hsp.hit_all[0].seq[:40]
)
self.assertEqual(
"AG-GACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGA", hsp.query_all[0].seq[-40:]
)
self.assertEqual(
"|| ||| |||||| || ||| || || ||| ||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"AGTGAC--CCCAGAGGAGCCAAGCAAAAAGA---TTCGGA", hsp.hit_all[0].seq[-40:]
)
# last block
self.assertEqual(
"AATAAGACTACCACGGACTTTTTACTATGTTCTTTAAAAA", hsp.query_all[-1].seq[:40]
)
self.assertEqual(
"||||||| | ||| | |||| | | | | || ",
hsp[-1].aln_annotation["similarity"][:40],
)
self.assertEqual(
"AATAAGAGCAACACAG----TTTA-TCTTATATGTA----", hsp.hit_all[-1].seq[:40]
)
self.assertEqual(
"CTGCAAGAACAACAGAAAAGGGAAAACGAAAAAGGAACAA", hsp.query_all[-1].seq[-40:]
)
self.assertEqual(
"| | | || | | || || |||||||| || ||||",
hsp[-1].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CCACTAAAAAATTATAAGAGCCAAAACGAAGTAGATACAA", hsp.hit_all[-1].seq[-40:]
)
def test_exn_22_m_coding2coding_fshifts(self):
"""Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn)."""
exn_file = get_file("exn_22_m_coding2coding_fshifts.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("coding2coding", qresult.model)
self.assertEqual(1, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|296143771|ref|NM_001180731.1|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
hit.description,
)
self.assertEqual(2, len(hit))
# first hit, first hsp
hsp = qresult[0][0]
self.assertEqual(213, hsp.score)
self.assertEqual([1, 1, 1, 1], hsp.query_strand_all)
self.assertEqual([1, 1, 1, 1], hsp.hit_strand_all)
self.assertEqual(0, hsp.query_start)
self.assertEqual(465, hsp.hit_start)
self.assertEqual(160, hsp.query_end)
self.assertEqual(630, hsp.hit_end)
self.assertEqual(
[(0, 93), (94, 127), (127, 139), (139, 160)], hsp.query_range_all
)
self.assertEqual(
[(465, 558), (558, 591), (593, 605), (609, 630)], hsp.hit_range_all
)
self.assertEqual([(93, 94), (127, 127), (139, 139)], hsp.query_inter_ranges)
self.assertEqual([(558, 558), (591, 593), (605, 609)], hsp.hit_inter_ranges)
self.assertEqual([1, 2, 2, 2], hsp.query_frame_all)
self.assertEqual([1, 1, 3, 1], hsp.hit_frame_all)
self.assertEqual(4, len(hsp.query_all))
self.assertEqual(4, len(hsp.hit_all))
self.assertEqual(4, len(hsp.aln_annotation_all))
# first block
self.assertEqual(
"ACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAAG", hsp[0].query.seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAAG", hsp[0].hit.seq[:40]
)
self.assertEqual(
"TATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACC", hsp[0].query.seq[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACC", hsp[0].hit.seq[-40:]
)
# last block
self.assertEqual("GACGAAAGTATTAATGGTAGT", hsp[-1].query.seq)
self.assertEqual("|||||||||||||||||||||", hsp[-1].aln_annotation["similarity"])
self.assertEqual("GACGAAAGTATTAATGGTAGT", hsp[-1].hit.seq)
# first hit, second hsp
hsp = qresult[0][1]
self.assertEqual(201, hsp.score)
self.assertEqual([-1, -1], hsp.query_strand_all)
self.assertEqual([-1, -1], hsp.hit_strand_all)
self.assertEqual(1, hsp.query_start)
self.assertEqual(466, hsp.hit_start)
self.assertEqual(158, hsp.query_end)
self.assertEqual(628, hsp.hit_end)
self.assertEqual([(95, 158), (1, 94)], hsp.query_range_all)
self.assertEqual([(559, 628), (466, 559)], hsp.hit_range_all)
self.assertEqual([(94, 95)], hsp.query_inter_ranges)
self.assertEqual([(559, 559)], hsp.hit_inter_ranges)
self.assertEqual([-3, -2], hsp.query_frame_all)
self.assertEqual([-2, -2], hsp.hit_frame_all)
self.assertEqual(2, len(hsp.query_all))
self.assertEqual(2, len(hsp.hit_all))
self.assertEqual(2, len(hsp.aln_annotation_all))
# first block
self.assertEqual(
"TACCATTAATACTTTCGTCATGGT<-><->AACGGCATGT", hsp[0].query.seq[:40]
)
self.assertEqual(
"||||||||||||||||||||+ ! ... !:!!|",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TACCATTAATACTTTCGTCACCGATGGTAACGGCACCTGT", hsp[0].hit.seq[:40]
)
# last block
self.assertEqual(
"TGGTTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACAT", hsp[-1].query.seq[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[-1].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TGGTTAAACTGGGAGCGTTCCATGAGCCTATGTTCCACAT", hsp[-1].hit.seq[:40]
)
def test_exn_22_m_protein2dna_fshifts(self):
"""Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn)."""
exn_file = get_file("exn_22_m_protein2dna_fshifts.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("sp|P24813|YAP2_YEAST", qresult.id)
self.assertEqual(
"AP-1-like transcription activator YAP2 OS=Saccharomyces cerevisiae (strain"
" ATCC 204508 / S288c) GN=CAD1 PE=1 SV=2",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("protein2dna:local", qresult.model)
self.assertEqual(1, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|296143771|ref|NM_001180731.1|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds",
hit.description,
)
self.assertEqual(2, len(hit))
# first hit, first hsp
hsp = qresult[0][0]
self.assertEqual(367, hsp.score)
self.assertEqual([0, 0], hsp.query_strand_all)
self.assertEqual([1, 1], hsp.hit_strand_all)
self.assertEqual(330, hsp.query_start)
self.assertEqual(216, hsp.hit_start)
self.assertEqual(409, hsp.query_end)
self.assertEqual(455, hsp.hit_end)
self.assertEqual([(330, 373), (373, 409)], hsp.query_range_all)
self.assertEqual([(216, 345), (347, 455)], hsp.hit_range_all)
self.assertEqual([(373, 373)], hsp.query_inter_ranges)
self.assertEqual([(345, 347)], hsp.hit_inter_ranges)
self.assertEqual([0, 0], hsp.query_frame_all)
self.assertEqual([1, 3], hsp.hit_frame_all)
self.assertEqual(2, len(hsp.query_all))
self.assertEqual(2, len(hsp.hit_all))
self.assertEqual(2, len(hsp.aln_annotation_all))
# first block
self.assertEqual(
"HTKTIRTQSEAIEHISSAISNGKASCYHILEEISSLPKYS", hsp[0].query.seq[:40]
)
self.assertEqual(
"HTKTIRTQSEAIEHISSAISNGKASCYHILEEISSLPKYS", hsp[0].hit.seq[:40]
)
self.assertEqual(
"TIRTQSEAIEHISSAISNGKASCYHILEEISSLPKYSSLD", hsp[0].query.seq[-40:]
)
self.assertEqual(
"TIRTQSEAIEHISSAISNGKASCYHILEEISSLPKYSSLD", hsp[0].hit.seq[-40:]
)
# last block
self.assertEqual("IDDLCSELIIKAKCTDDCKIVVKARDLQSALVRQLL", hsp[-1].query.seq)
self.assertEqual("IDDLCSELIIKAKCTDDCKIVVKARDLQSALVRQLL", hsp[-1].hit.seq)
# first hit, second hsp
hsp = qresult[0][1]
self.assertEqual(322, hsp.score)
self.assertEqual([0], hsp.query_strand_all)
self.assertEqual([1], hsp.hit_strand_all)
self.assertEqual(6, hsp.query_start)
self.assertEqual(16, hsp.hit_start)
self.assertEqual(70, hsp.query_end)
self.assertEqual(208, hsp.hit_end)
self.assertEqual([(6, 70)], hsp.query_range_all)
self.assertEqual([(16, 208)], hsp.hit_range_all)
self.assertEqual([], hsp.query_inter_ranges)
self.assertEqual([], hsp.hit_inter_ranges)
self.assertEqual([0], hsp.query_frame_all)
self.assertEqual([2], hsp.hit_frame_all)
self.assertEqual(1, len(hsp.query_all))
self.assertEqual(1, len(hsp.hit_all))
self.assertEqual(1, len(hsp.aln_annotation_all))
self.assertEqual(
"KGQQIYLAGDMKKQMLLNKDGTPKRKVGRPGRKRIDSEAK", hsp[0].query.seq[:40]
)
self.assertEqual(
"KGQQIYLAGDMKKQMLLNKDGTPKRKVGRPGRKRIDSEAK", hsp[0].hit.seq[:40]
)
self.assertEqual(
"RKVGRPGRKRIDSEAKSRRTAQNRAAQRAFRDRKEAKMKS", hsp[0].query.seq[-40:]
)
self.assertEqual(
"RKVGRPGRKRIDSEAKSRRTAQNRAAQRAFRDRKEAKMKS", hsp[0].hit.seq[-40:]
)
def test_exn_22_m_protein2genome(self):
"""Test parsing exonerate output (exn_22_m_protein2genome.exn)."""
exn_file = get_file("exn_22_m_protein2genome.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("sp|P24813|YAP2_YEAST", qresult.id)
self.assertEqual(
"AP-1-like transcription activator YAP2 OS=Saccharomyces cerevisiae (strain"
" ATCC 204508 / S288c) GN=CAD1 PE=1 SV=2",
qresult.description,
)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("protein2genome:local", qresult.model)
self.assertEqual(3, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome IV, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit))
# first hit, first hsp
hsp = qresult[0][0]
self.assertEqual(2105, hsp.score)
self.assertEqual(0, hsp.query_strand)
self.assertEqual(-1, hsp.hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1318048, hsp.hit_start)
self.assertEqual(409, hsp.query_end)
self.assertEqual(1319275, hsp.hit_end)
self.assertEqual(
"MGNILRKGQQIYLAGDMKKQMLLNKDGTPKRKVGRPGRKR", hsp[0].query.seq[:40]
)
self.assertEqual(
"MGNILRKGQQIYLAGDMKKQMLLNKDGTPKRKVGRPGRKR", hsp[0].hit.seq[:40]
)
self.assertEqual(
"SSLDIDDLCSELIIKAKCTDDCKIVVKARDLQSALVRQLL", hsp[0].query.seq[-40:]
)
self.assertEqual(
"SSLDIDDLCSELIIKAKCTDDCKIVVKARDLQSALVRQLL", hsp[0].hit.seq[-40:]
)
# last hit
hit = qresult[-1]
self.assertEqual("gi|330443590|ref|NC_001140.6|", hit.id)
self.assertEqual(
"Saccharomyces cerevisiae S288c chromosome VIII, complete sequence",
hit.description,
)
self.assertEqual(1, len(hit))
# last hit, first hsp
hsp = qresult[-1][0]
self.assertEqual(122, hsp.score)
self.assertEqual([0, 0], hsp.query_strand_all)
self.assertEqual([-1, -1], hsp.hit_strand_all)
self.assertEqual("RKRIDSEAKSRRTAQNRAAQRAFRDRKEAKMKSLQERX", hsp[0].query.seq)
self.assertEqual("NENVPDDSKAKKKAQNRAAQKAFRERKEARMKELQDKX", hsp[0].hit.seq)
self.assertEqual("!.!", hsp.aln_annotation_all[0]["similarity"][0])
self.assertEqual(":!", hsp.aln_annotation_all[0]["similarity"][-1])
self.assertEqual("AAT", hsp.aln_annotation_all[0]["hit_annotation"][0])
self.assertEqual("TT", hsp.aln_annotation_all[0]["hit_annotation"][-1])
self.assertEqual(
"XELLEQKDAQNKTTTDFLLCSLKSLLSEITKYRAKNSDDERILAFLDDLQE", hsp[-1].query.seq
)
self.assertEqual(
"XNKILNRDPQFMSNSSFHQCVSLDSINTIEKDEEKNSDDDAGLQAATDARE", hsp[-1].hit.seq
)
self.assertEqual("!", hsp.aln_annotation_all[-1]["similarity"][0])
self.assertEqual("|||", hsp.aln_annotation_all[-1]["similarity"][-1])
self.assertEqual("A", hsp.aln_annotation_all[-1]["hit_annotation"][0])
self.assertEqual("GAA", hsp.aln_annotation_all[-1]["hit_annotation"][-1])
self.assertEqual([(37, 74), (75, 125)], hsp.query_range_all)
self.assertEqual([(84533, 84646), (68450, 68601)], hsp.hit_range_all)
self.assertEqual([(74, 75)], hsp.query_inter_ranges)
self.assertEqual([(68601, 84533)], hsp.hit_inter_ranges)
self.assertEqual([0, 0], hsp.query_frame_all)
self.assertEqual([-3, -3], hsp.hit_frame_all)
self.assertEqual(2, len(hsp.query_all))
self.assertEqual(2, len(hsp.hit_all))
self.assertEqual(2, len(hsp.aln_annotation_all))
def test_exn_24_m_protein2genome_revcomp_fshifts(self):
"""Test parsing exonerate output (exn_24_m_protein2genome_revcomp_fshifts.exn)."""
exn_file = get_file("exn_24_m_protein2genome_revcomp_fshifts.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("Morus-gene026", qresult.id)
self.assertEqual("", qresult.description)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("protein2genome:local", qresult.model)
self.assertEqual(1, len(qresult))
# first (only) hit
hit = qresult[0]
self.assertEqual("NODE_2_length_1708_cov_48.590765", hit.id)
self.assertEqual("SPAdes NODE_2 contig", hit.description)
self.assertEqual(1, len(hit))
# first hit, first hsp
hsp = qresult[0][0]
self.assertEqual(1308, hsp.score)
self.assertEqual([0, 0], hsp.query_strand_all)
self.assertEqual([-1, -1], hsp.hit_strand_all)
self.assertEqual(69, hsp.query_start)
self.assertEqual(331, hsp.hit_start)
self.assertEqual(441, hsp.query_end)
self.assertEqual(1416, hsp.hit_end)
self.assertEqual([(69, 402), (402, 441)], hsp.query_range_all)
self.assertEqual([(450, 1416), (331, 448)], hsp.hit_range_all)
self.assertEqual([(402, 402)], hsp.query_inter_ranges)
self.assertEqual([(448, 450)], hsp.hit_inter_ranges)
self.assertEqual([0, 0], hsp.query_frame_all)
self.assertEqual([-1, -2], hsp.hit_frame_all)
self.assertEqual(2, len(hsp.query_all))
self.assertEqual(2, len(hsp.hit_all))
self.assertEqual(2, len(hsp.aln_annotation_all))
# first block
self.assertEqual(
"PESPWTCSPLQT--PSPSLLYHCIASLHRHDGTIHSIAVS", hsp[0].query.seq[:40]
)
self.assertEqual(
"PESPWTSSPLQTLSHSPSLLYHCIASLRRHDGTIYSIATS", hsp[0].hit.seq[:40]
)
self.assertEqual(
"VEKMVFSGSEDTTIRIWRREEGSCLHECLAVLDGHRGPVK", hsp[0].query.seq[-40:]
)
self.assertEqual(
"VEKMVFGGSEDTTIRIWRREEGGCFHKCLAVLDGHRXXXX", hsp[0].hit.seq[-40:]
)
# last block
self.assertEqual("CLAACLEVEKVVMMGFLVYSASLDQTFKVWRVKVLPDEE", hsp[-1].query.seq)
self.assertEqual("CLAAC*QVEKMVMMGFLIYSVSLDQTLKVWRVKILPDQE", hsp[-1].hit.seq)
def test_exn_24_protein2genome_met_intron(self):
"""Test parsing exonerate output (exn_24_m_protein2genome_met_intron.exn)."""
exn_file = get_file("exn_24_m_protein2genome_met_intron.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("Morus-gene001", qresult.id)
self.assertEqual("", qresult.description)
self.assertEqual("exonerate", qresult.program)
self.assertEqual("protein2genome:local", qresult.model)
self.assertEqual(1, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("NODE_1_length_2817_cov_100.387732", hit.id)
self.assertEqual("SPAdes contig NODE_1", hit.description)
self.assertEqual(1, len(hit))
# first hit, first hsp
self.assertEqual(1978, hsp.score)
self.assertEqual([0, 0, 0, 0, 0, 0], hsp.query_strand_all)
self.assertEqual([-1, -1, -1, -1, -1, -1], hsp.hit_strand_all)
self.assertEqual(48, hsp.query_start)
self.assertEqual(388, hsp.hit_start)
self.assertEqual(482, hsp.query_end)
self.assertEqual(2392, hsp.hit_end)
self.assertEqual(
[(48, 85), (85, 118), (118, 155), (155, 256), (257, 303), (303, 482)],
hsp.query_range_all,
)
self.assertEqual(
[
(2281, 2392),
(2030, 2129),
(1810, 1921),
(1420, 1724),
(1058, 1198),
(388, 925),
],
hsp.hit_range_all,
)
self.assertEqual(
[(2129, 2281), (1921, 2030), (1724, 1810), (1198, 1420), (925, 1058)],
hsp.hit_inter_ranges,
)
self.assertEqual(
[(85, 85), (118, 118), (155, 155), (256, 257), (303, 303)],
hsp.query_inter_ranges,
)
self.assertEqual("MVQTPLHVSAGNNRADIVKF", hsp[0].query.seq[:20])
self.assertEqual("VKFLLEFPGPEKVELEAKNM", hsp[0].query.seq[-20:])
self.assertEqual("|||", hsp[0].aln_annotation["similarity"][0])
self.assertEqual("|||", hsp[0].aln_annotation["similarity"][-1])
self.assertEqual("ATG", hsp[0].aln_annotation["hit_annotation"][0])
self.assertEqual("ATG", hsp[0].aln_annotation["hit_annotation"][-1])
self.assertEqual([0, 0, 0, 0, 0, 0], hsp.query_frame_all)
self.assertEqual([-2, -3, -2, -2, -3, -2], hsp.hit_frame_all)
self.assertEqual(6, len(hsp.query_all))
self.assertEqual(6, len(hsp.hit_all))
self.assertEqual(6, len(hsp.aln_annotation_all))
def test_exn_22_q_none(self):
"""Test parsing exonerate output (exn_22_q_none.exn)."""
exn_file = get_file("exn_22_q_none.exn")
qresults = parse(exn_file, "exonerate-text")
self.assertRaises(StopIteration, next, qresults)
class ExonerateVulgarCases(unittest.TestCase):
fmt = "exonerate-vulgar"
def test_exn_22_o_vulgar(self):
"""Test parsing exonerate output (exn_22_o_vulgar.exn)."""
exn_file = get_file("exn_22_o_vulgar.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("sacCer3_dna", qresult.id)
self.assertEqual("<unknown description>", qresult.description)
self.assertEqual("exonerate", qresult.program)
self.assertEqual(3, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual("<unknown description>", hit.description)
self.assertEqual(2, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(2641, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1319468, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(1319997, hsp.hit_end)
self.assertEqual([(0, 529)], hsp.query_range_all[:5])
self.assertEqual([(1319468, 1319997)], hsp.hit_range_all[:5])
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(" M 26 26 C 3 3 M 500 500", hsp.vulgar_comp)
# first hit, second hsp
hsp = qresult[0].hsps[1]
self.assertEqual(2641, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1319468, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(1319997, hsp.hit_end)
self.assertEqual([(0, 529)], hsp.query_range_all[:5])
self.assertEqual([(1319468, 1319997)], hsp.hit_range_all[:5])
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(" M 90 90 C 3 3 M 436 436", hsp.vulgar_comp)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443489|ref|NC_001135.5|", hit.id)
self.assertEqual("<unknown description>", hit.description)
self.assertEqual(1, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(267, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(162, hsp.query_start)
self.assertEqual(23668, hsp.hit_start)
self.assertEqual(491, hsp.query_end)
self.assertEqual(115569, hsp.hit_end)
self.assertEqual(
[(462, 491), (413, 462), (378, 413), (302, 378), (162, 302)],
hsp.query_range_all[:5],
)
self.assertEqual(
[
(23668, 23697),
(32680, 32732),
(42287, 42325),
(97748, 97821),
(115419, 115569),
],
hsp.hit_range_all[:5],
)
self.assertEqual([(378, 379), (376, 378)], hsp.query_split_codons)
self.assertEqual([(42324, 42325), (97748, 97750)], hsp.hit_split_codons)
self.assertEqual(
" M 29 29 5 0 2 I 0 8979 3 0 2 M 32 32 G 0 2 M 2 2 G 0 1 M 15 15 5 0 2 I 0 "
"9551 3 0 2 M 3 3 G 1 0 M 5 5 G 0 2 M 3 3 G 0 1 M 4 4 G 0 1 M 18 18 S 1 1 "
"5 0 2 I 0 55419 3 0 2 S 2 2 C 3 3 M 22 22 G 3 0 M 46 46 5 0 2 I 0 17594 "
"3 0 2 M 14 14 G 0 1 M 9 9 G 1 0 M 15 15 G 0 3 M 17 17 G 0 3 M 1 1 G 0 1 "
"M 13 13 G 0 1 M 6 6 G 1 0 M 12 12 G 0 2 M 45 45 G 0 1 M 6 6",
hsp.vulgar_comp,
)
# third hit
hit = qresult[2]
self.assertEqual("gi|330443667|ref|NC_001143.9|", hit.id)
self.assertEqual("<unknown description>", hit.description)
self.assertEqual(1, len(hit.hsps))
# third hit, first hsp
hsp = qresult[2].hsps[0]
self.assertEqual(267, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(78, hsp.query_start)
self.assertEqual(71883, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(641760, hsp.hit_end)
self.assertEqual(
[(449, 529), (319, 388), (198, 284), (161, 198), (78, 114)],
hsp.query_range_all[:5],
)
self.assertEqual(
[
(641682, 641760),
(487327, 487387),
(386123, 386207),
(208639, 208677),
(71883, 71917),
],
hsp.hit_range_all[:5],
)
self.assertEqual([(198, 200), (197, 198)], hsp.query_split_codons)
self.assertEqual([(386123, 386125), (208676, 208677)], hsp.hit_split_codons)
self.assertEqual(
" M 31 31 G 3 0 M 4 4 G 2 0 M 19 19 G 0 3 M 9 9 G 0 1 M 6 6 G 1 0 M 5 5 5 "
"2 2 I 0 154244 I 57 0 I 0 47 3 2 2 M 25 25 G 5 0 M 4 4 G 1 0 M 3 3 G 3 0 "
"M 4 4 G 1 0 M 9 9 G 0 1 M 14 14 5 2 2 I 0 101116 I 31 0 3 2 2 M 23 23 G "
"0 1 M 15 15 G 1 0 M 9 9 G 1 0 M 2 2 G 1 0 M 14 14 C 18 18 S 2 2 5 0 2 I "
"0 177442 3 0 2 S 1 1 C 12 12 M 2 2 G 0 1 M 22 22 5 2 2 I 0 136697 I 7 0 "
"I 0 6 I 1 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 2 0 I 0 1 I 1 0 "
"I 0 1 I 1 0 I 0 1 I 3 0 I 0 1 I 2 0 I 0 1 I 1 0 I 0 1 I 1 0 I 0 1 I 2 0 "
"I 0 2 I 2 0 I 0 2 I 17 0 3 2 2 M 12 12 G 2 0 M 22 22",
hsp.vulgar_comp,
)
def test_exn_22_o_vulgar_fshifts(self):
"""Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn)."""
exn_file = get_file("exn_22_o_vulgar_fshifts.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("gi|296143771|ref|NM_001180731.1|", qresult.id)
self.assertEqual("<unknown description>", qresult.description)
self.assertEqual("exonerate", qresult.program)
self.assertEqual(1, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|296143771|ref|NM_001180731.1|", hit.id)
self.assertEqual("<unknown description>", hit.description)
self.assertEqual(2, len(hit))
# first hit, first hsp
hsp = qresult[0][0]
self.assertEqual(213, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(465, hsp.hit_start)
self.assertEqual(160, hsp.query_end)
self.assertEqual(630, hsp.hit_end)
self.assertEqual(
[(0, 93), (94, 127), (127, 139), (139, 160)], hsp.query_range_all[:5]
)
self.assertEqual(
[(465, 558), (558, 591), (593, 605), (609, 630)], hsp.hit_range_all[:5]
)
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(
" C 93 93 F 1 0 C 33 33 F 0 2 C 12 12 F 0 4 C 21 21", hsp.vulgar_comp
)
# first hit, second hsp
hsp = qresult[0][1]
self.assertEqual(201, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(1, hsp.query_start)
self.assertEqual(466, hsp.hit_start)
self.assertEqual(158, hsp.query_end)
self.assertEqual(628, hsp.hit_end)
self.assertEqual([(95, 158), (1, 94)], hsp.query_range_all[:5])
self.assertEqual([(559, 628), (466, 559)], hsp.hit_range_all[:5])
self.assertEqual([], hsp.query_split_codons)
self.assertEqual([], hsp.hit_split_codons)
self.assertEqual(" C 24 24 G 0 6 C 39 39 F 1 0 C 93 93", hsp.vulgar_comp)
class ExonerateCigarCases(unittest.TestCase):
fmt = "exonerate-cigar"
def test_exn_22_o_vulgar_cigar(self):
"""Test parsing exonerate output (exn_22_o_vulgar_cigar.exn)."""
exn_file = get_file("exn_22_o_vulgar_cigar.exn")
qresult = read(exn_file, self.fmt)
# check common attributes
for hit in qresult:
self.assertEqual(qresult.id, hit.query_id)
for hsp in hit:
self.assertEqual(hit.id, hsp.hit_id)
self.assertEqual(qresult.id, hsp.query_id)
self.assertEqual("sacCer3_dna", qresult.id)
self.assertEqual("<unknown description>", qresult.description)
self.assertEqual("exonerate", qresult.program)
self.assertEqual(3, len(qresult))
# first hit
hit = qresult[0]
self.assertEqual("gi|330443520|ref|NC_001136.10|", hit.id)
self.assertEqual("<unknown description>", hit.description)
self.assertEqual(2, len(hit.hsps))
# first hit, first hsp
hsp = qresult[0].hsps[0]
self.assertEqual(2641, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1319468, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(1319997, hsp.hit_end)
self.assertEqual(" M 26 M 3 M 500", hsp.cigar_comp)
# first hit, second hsp
hsp = qresult[0].hsps[1]
self.assertEqual(2641, hsp.score)
self.assertEqual(1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(0, hsp.query_start)
self.assertEqual(1319468, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(1319997, hsp.hit_end)
self.assertEqual(" M 90 M 3 M 436", hsp.cigar_comp)
# second hit
hit = qresult[1]
self.assertEqual("gi|330443489|ref|NC_001135.5|", hit.id)
self.assertEqual("<unknown description>", hit.description)
self.assertEqual(1, len(hit.hsps))
# second hit, first hsp
hsp = qresult[1].hsps[0]
self.assertEqual(267, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(1, hsp[0].hit_strand)
self.assertEqual(162, hsp.query_start)
self.assertEqual(23668, hsp.hit_start)
self.assertEqual(491, hsp.query_end)
self.assertEqual(115569, hsp.hit_end)
self.assertEqual(
" M 29 D 8983 M 32 D 2 M 2 D 1 M 15 D 9555 M 3 I 1 M 5 D 2 M 3 D 1 M 4 D "
"1 M 18 M 1 D 55423 M 5 M 22 I 3 M 46 D 17598 M 14 D 1 M 9 I 1 M 15 D 3 M "
"17 D 3 M 1 D 1 M 13 D 1 M 6 I 1 M 12 D 2 M 45 D 1 M 6",
hsp.cigar_comp,
)
# third hit
hit = qresult[2]
self.assertEqual("gi|330443667|ref|NC_001143.9|", hit.id)
self.assertEqual("<unknown description>", hit.description)
self.assertEqual(1, len(hit.hsps))
# third hit, first hsp
hsp = qresult[2].hsps[0]
self.assertEqual(267, hsp.score)
self.assertEqual(-1, hsp[0].query_strand)
self.assertEqual(-1, hsp[0].hit_strand)
self.assertEqual(78, hsp.query_start)
self.assertEqual(71883, hsp.hit_start)
self.assertEqual(529, hsp.query_end)
self.assertEqual(641760, hsp.hit_end)
self.assertEqual(
" M 31 I 3 M 4 I 2 M 19 D 3 M 9 D 1 M 6 I 1 M 7 D 154244 I 57 D 47 M 27 I "
"5 M 4 I 1 M 3 I 3 M 4 I 1 M 9 D 1 M 16 D 101116 I 31 M 25 D 1 M 15 I 1 M "
"9 I 1 M 2 I 1 M 14 M 20 D 177446 M 13 M 2 D 1 M 24 D 136697 I 7 D 6 I 1 D "
"1 I 1 D 1 I 1 D 1 I 1 D 1 I 2 D 1 I 1 D 1 I 1 D 1 I 3 D 1 I 2 D 1 I 1 D 1 "
"I 1 D 1 I 2 D 2 I 2 D 2 I 17 M 14 I 2 M 22",
hsp.cigar_comp,
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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