forked from biopython/biopython
/
test_SearchIO_exonerate.py
2564 lines (2456 loc) · 104 KB
/
test_SearchIO_exonerate.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, 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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||| |||| ||||| ||| | | ||| ||| | |||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACCGAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGAT", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"AAGTTATGTGGAACA--TAGGCTCATGGAACGCTCCCAGT", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"| || | | |||| || ||| || | ||| |||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"ATGT--GGGGAAACAATTACCTTCACCAAATGATCCAAGT", str(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-", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||| || || || | ||||| | |||| || | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGATGATATATTA-GATGGGG-ATG-AAGATGAGCCAGA", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"G-TATAGAAGTACAGCCGCACACTCAAGAGAATGAGAAAG", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"| | ||||| | | | | | | ||| | |||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GTTGAAGAAGCCAAACGGAAGAAAGACGAGGA-GAGAAAG", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"CTACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGA", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"CTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCAT", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"|||| || | |||| | |||||| |||| | | | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGTGAACCT-CTTCAAGACGGTCAG--AATA-A-TCAA", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"AGCAAATATATTTAGCAGGTGACATGAAGAAGCAAATGTT", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"|| |||| | | | |||| ||||||||||||| | |",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"AG--AATA-A-TCAACAGG----ATGAAGAAGCAAAAGAT", str(hsp.hit_all[0].seq)[-40:]
)
# last block
self.assertEqual(
"TATTAGCCTTCC--TCGATGATCTGCA--A-GAACAACAG", str(hsp.query_all[-1].seq)[:40]
)
self.assertEqual(
"| |||| || | ||||| | || || | ||| | | ",
hsp[-1].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TCATAGCGTTACGTTCGAT-ACCTTCACTACGAAGATCCA", str(hsp.hit_all[-1].seq)[:40]
)
self.assertEqual(
"AAGTATAGAAGTACAGCCGCACACTCAAGAGAATGAGAAA", str(hsp.query_all[-1].seq)[-40:]
)
self.assertEqual(
" ||||||||||||| || ||| | || | |||",
hsp[-1].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TTCTATAGAAGTACAGTTATTCAAACAAAAAAAAAAAAAA", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGC", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||+! .!.||| !!:...||+:!::!:! ||+||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TGTTCGGAAATTTGGGATAGAATAACAACACATCCGAAAT", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"CAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTC", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"!!!.||+...|||:!:||+ |||+|| !!::!!.:!:",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CAATGCAGAAGACGTTCAATTAGCTTTGAATAAGCATATG", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACAGGAGCTGTCTAACCAGAGCACTCTGTAAGTCGCGAGC", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"GCTAAATATATTTGCTGACCTTTCCGAAGGATATTGCCCA", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||+! .!.||| !!:...||+:!::!:! ||+||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"TGTTCGGAAATTTGGGATAGAATAACAACACATCCGAAAT", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"CAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTC", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"!!!.||+...|||:!:||+ |||+|| !!::!!.:!:",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CAATGCAGAAGACGTTCAATTAGCTTTGAATAAGCATATG", str(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", str(hsp[0].query.seq)[:40])
self.assertEqual(
["|||", "...", " !!", " !!", "! !"], hsp[0].aln_annotation["similarity"][:5]
)
self.assertEqual("NQSVPKRPAGSVQNPVYHNQPLNPAPSRDPH", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAG", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"TCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"|||| || | |||| | |||||| |||| | | | ",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ATGGTGAACCT-CTTCAAGACGGTCAG--AATA-A-TCAA", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"AGCAAATATATTTAGCAGGTGACATGAAGAAGCAAATGTT", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"|| |||| | | | |||| ||||||||||||| | |",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"AG--AATA-A-TCAACAGG----ATGAAGAAGCAAAAGAT", str(hsp.hit_all[0].seq)[-40:]
)
# last block
self.assertEqual("AGCTAAGAATTCTGATGATG-----AAAGAA", str(hsp.query_all[-1].seq))
self.assertEqual(
"| |||||||||||| ||| ||||||", hsp[-1].aln_annotation["similarity"]
)
self.assertEqual("ATGGAAGAATTCTGATAATGCTGTAAAAGAA", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"| |||| ||| | |||| | | || |||| | | |",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(
"ACCAAAGATAACAAGGCAG--AAAAAGAGGAAGAAGAAAT", str(hsp.hit_all[0].seq)[:40]
)
self.assertEqual(
"AG-GACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGA", str(hsp.query_all[0].seq)[-40:]
)
self.assertEqual(
"|| ||| |||||| || ||| || || ||| ||",
hsp[0].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"AGTGAC--CCCAGAGGAGCCAAGCAAAAAGA---TTCGGA", str(hsp.hit_all[0].seq)[-40:]
)
# last block
self.assertEqual(
"AATAAGACTACCACGGACTTTTTACTATGTTCTTTAAAAA", str(hsp.query_all[-1].seq)[:40]
)
self.assertEqual(
"||||||| | ||| | |||| | | | | || ",
hsp[-1].aln_annotation["similarity"][:40],
)
self.assertEqual(
"AATAAGAGCAACACAG----TTTA-TCTTATATGTA----", str(hsp.hit_all[-1].seq)[:40]
)
self.assertEqual(
"CTGCAAGAACAACAGAAAAGGGAAAACGAAAAAGGAACAA", str(hsp.query_all[-1].seq)[-40:]
)
self.assertEqual(
"| | | || | | || || |||||||| || ||||",
hsp[-1].aln_annotation["similarity"][-40:],
)
self.assertEqual(
"CCACTAAAAAATTATAAGAGCCAAAACGAAGTAGATACAA", str(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", str(hsp.query_all[0].seq)[:40]
)
self.assertEqual(
"||||||||||||||||||||||||||||||||||||||||",
hsp[0].aln_annotation["similarity"][:40],
)
self.assertEqual(