# 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", 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("", 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("", 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("", 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("", 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("", 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("", 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("", 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("", 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("", 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("", 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)