# Copyright 2004 by Frank Kauff. All rights reserved. # Revisions copyright 2008-2013 by Peter Cock. All rights reserved. # Revisions copyright 2009-2009 by Michiel de Hoon. 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 Ace module.""" import unittest from Bio.Sequencing import Ace class AceTestOne(unittest.TestCase): def setUp(self): self.handle = open("Ace/contig1.ace") def tearDown(self): self.handle.close() def test_check_ACEParser(self): """Test to check that ACEParser can parse the whole file into one record.""" record = Ace.read(self.handle) self.assertEqual(record.ncontigs, 2) self.assertEqual(record.nreads, 16) self.assertEqual(len(record.wa), 1) self.assertEqual(record.wa[0].tag_type, "phrap_params") self.assertEqual(record.wa[0].program, "phrap") self.assertEqual(record.wa[0].date, "040203:114710") self.assertEqual( record.wa[0].info, [ "phrap 304_nuclsu.fasta.screen -new_ace -retain_duplicates", "phrap version 0.990329", ], ) self.assertEqual(len(record.contigs), 2) self.assertEqual(len(record.contigs[0].reads), 2) self.assertEqual(record.contigs[0].name, "Contig1") self.assertEqual(record.contigs[0].nbases, 856) self.assertEqual(record.contigs[0].nreads, 2) self.assertEqual(record.contigs[0].nsegments, 31) self.assertEqual(record.contigs[0].uorc, "U") center = len(record.contigs[0].sequence) // 2 self.assertEqual(record.contigs[0].sequence[:10], "aatacgGGAT") self.assertEqual( record.contigs[0].sequence[center - 5 : center + 5], "ACATCATCTG" ) self.assertEqual(record.contigs[0].sequence[-10:], "cATCTAGtac") center = len(record.contigs[0].quality) // 2 self.assertEqual( record.contigs[0].quality[:10], [0, 0, 0, 0, 0, 0, 22, 23, 25, 28] ) self.assertEqual( record.contigs[0].quality[center - 5 : center + 5], [90, 90, 90, 90, 90, 90, 90, 90, 90, 90], ) self.assertEqual( record.contigs[0].quality[-10:], [15, 22, 30, 24, 28, 22, 21, 15, 19, 0] ) self.assertEqual(len(record.contigs[0].af), 2) self.assertEqual(record.contigs[0].af[1].name, "BL060c3-LR0R.b.ab1") self.assertEqual(record.contigs[0].af[1].coru, "U") self.assertEqual(record.contigs[0].af[1].padded_start, 1) self.assertEqual(len(record.contigs[0].bs), 31) self.assertEqual(record.contigs[0].bs[15].name, "BL060c3-LR5.g.ab1") self.assertEqual(record.contigs[0].bs[15].padded_start, 434) self.assertEqual(record.contigs[0].bs[15].padded_end, 438) self.assertEqual(record.contigs[0].bs[30].name, "BL060c3-LR0R.b.ab1") self.assertEqual(record.contigs[0].bs[30].padded_start, 823) self.assertEqual(record.contigs[0].bs[30].padded_end, 856) self.assertEqual(len(record.contigs[0].ct), 1) self.assertEqual(record.contigs[0].ct[0].name, "Contig1") self.assertEqual(record.contigs[0].ct[0].tag_type, "repeat") self.assertEqual(record.contigs[0].ct[0].program, "phrap") self.assertEqual(record.contigs[0].ct[0].padded_start, 52) self.assertEqual(record.contigs[0].ct[0].padded_end, 53) self.assertEqual(record.contigs[0].ct[0].date, "555456:555432") self.assertEqual( record.contigs[0].ct[0].info, ["This is the forst line of comment for c1", "and this the second for c1"], ) self.assertIsNone(record.contigs[0].wa) self.assertEqual(len(record.contigs[0].reads), 2) self.assertEqual(record.contigs[0].reads[0].rd.name, "BL060c3-LR5.g.ab1") self.assertEqual(record.contigs[0].reads[0].rd.padded_bases, 868) self.assertEqual(record.contigs[0].reads[0].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[0].rd.read_tags, 0) center = len(record.contigs[0].reads[0].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[0].rd.sequence[:10], "tagcgaggaa") self.assertEqual( record.contigs[0].reads[0].rd.sequence[center - 5 : center + 5], "CCGAGGCCAA", ) self.assertEqual(record.contigs[0].reads[0].rd.sequence[-10:], "gaaccatcag") self.assertEqual(record.contigs[0].reads[0].qa.qual_clipping_start, 80) self.assertEqual(record.contigs[0].reads[0].qa.qual_clipping_end, 853) self.assertEqual(record.contigs[0].reads[0].qa.align_clipping_start, 22) self.assertEqual(record.contigs[0].reads[0].qa.align_clipping_end, 856) self.assertIsNone(record.contigs[0].reads[0].ds) self.assertEqual(len(record.contigs[0].reads[0].rt), 4) self.assertEqual(record.contigs[0].reads[0].rt[0].name, "BL060c3-LR5.g.ab1") self.assertEqual( record.contigs[0].reads[0].rt[0].tag_type, "matchElsewhereHighQual" ) self.assertEqual(record.contigs[0].reads[0].rt[0].program, "phrap") self.assertEqual(record.contigs[0].reads[0].rt[0].padded_start, 590) self.assertEqual(record.contigs[0].reads[0].rt[0].padded_end, 607) self.assertEqual(record.contigs[0].reads[0].rt[0].date, "040217:110357") self.assertEqual(record.contigs[0].reads[0].rt[1].name, "BL060c3-LR5.g.ab1") self.assertEqual( record.contigs[0].reads[0].rt[1].tag_type, "matchElsewhereHighQual" ) self.assertEqual(record.contigs[0].reads[0].rt[1].program, "phrap") self.assertEqual(record.contigs[0].reads[0].rt[1].padded_start, 617) self.assertEqual(record.contigs[0].reads[0].rt[1].padded_end, 631) self.assertEqual(record.contigs[0].reads[0].rt[1].date, "040217:110357") self.assertEqual(record.contigs[0].reads[0].rt[2].name, "BL060c3-LR5.g.ab1") self.assertEqual( record.contigs[0].reads[0].rt[2].tag_type, "matchElsewhereHighQual" ) self.assertEqual(record.contigs[0].reads[0].rt[2].program, "phrap") self.assertEqual(record.contigs[0].reads[0].rt[2].padded_start, 617) self.assertEqual(record.contigs[0].reads[0].rt[2].padded_end, 631) self.assertEqual(record.contigs[0].reads[0].rt[2].date, "040217:110357") self.assertEqual(record.contigs[0].reads[0].rt[3].name, "BL060c3-LR5.g.ab1") self.assertEqual( record.contigs[0].reads[0].rt[3].tag_type, "matchElsewhereHighQual" ) self.assertEqual(record.contigs[0].reads[0].rt[3].program, "phrap") self.assertEqual(record.contigs[0].reads[0].rt[3].padded_start, 617) self.assertEqual(record.contigs[0].reads[0].rt[3].padded_end, 631) self.assertEqual(record.contigs[0].reads[0].rt[3].date, "040217:110357") self.assertEqual(len(record.contigs[0].reads[0].wr), 1) self.assertEqual(record.contigs[0].reads[0].wr[0].name, "BL060c3-LR5.g.ab1") self.assertEqual(record.contigs[0].reads[0].wr[0].aligned, "unaligned") self.assertEqual(record.contigs[0].reads[0].wr[0].program, "phrap") self.assertEqual(record.contigs[0].reads[0].wr[0].date, "040217:110357") self.assertEqual(record.contigs[0].reads[1].rd.name, "BL060c3-LR0R.b.ab1") self.assertEqual(record.contigs[0].reads[1].rd.padded_bases, 856) self.assertEqual(record.contigs[0].reads[1].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[1].rd.read_tags, 0) center = len(record.contigs[0].reads[1].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[1].rd.sequence[:10], "aatacgGGAT") self.assertEqual( record.contigs[0].reads[1].rd.sequence[center - 5 : center + 5], "ACATCATCTG", ) self.assertEqual(record.contigs[0].reads[1].rd.sequence[-10:], "cATCTAGtac") self.assertEqual(record.contigs[0].reads[1].qa.qual_clipping_start, 7) self.assertEqual(record.contigs[0].reads[1].qa.qual_clipping_end, 778) self.assertEqual(record.contigs[0].reads[1].qa.align_clipping_start, 1) self.assertEqual(record.contigs[0].reads[1].qa.align_clipping_end, 856) self.assertIsNone(record.contigs[0].reads[1].ds) self.assertIsNone(record.contigs[0].reads[1].rt) self.assertIsNone(record.contigs[0].reads[1].wr) self.assertEqual(len(record.contigs[1].reads), 14) self.assertEqual(record.contigs[1].name, "Contig2") self.assertEqual(record.contigs[1].nbases, 3296) self.assertEqual(record.contigs[1].nreads, 14) self.assertEqual(record.contigs[1].nsegments, 214) self.assertEqual(record.contigs[1].uorc, "U") center = len(record.contigs[1].sequence) // 2 self.assertEqual(record.contigs[1].sequence[:10], "cacggatgat") self.assertEqual( record.contigs[1].sequence[center - 5 : center + 5], "TTTGAATATT" ) self.assertEqual(record.contigs[1].sequence[-10:], "Atccttgtag") center = len(record.contigs[1].quality) // 2 self.assertEqual(record.contigs[1].quality[:10], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) self.assertEqual( record.contigs[1].quality[center - 5 : center + 5], [90, 90, 90, 90, 90, 90, 90, 90, 90, 90], ) self.assertEqual( record.contigs[1].quality[-10:], [24, 0, 0, 0, 0, 0, 0, 0, 0, 0] ) self.assertEqual(len(record.contigs[1].af), 14) self.assertEqual(record.contigs[1].af[7].name, "BL060-LR3R.b.ab1") self.assertEqual(record.contigs[1].af[7].coru, "C") self.assertEqual(record.contigs[1].af[7].padded_start, 1601) self.assertEqual(record.contigs[1].af[13].name, "BL060c2-LR0R.b.ab1") self.assertEqual(record.contigs[1].af[13].coru, "C") self.assertEqual(record.contigs[1].af[13].padded_start, 2445) self.assertEqual(len(record.contigs[1].bs), 214) self.assertEqual(record.contigs[1].bs[107].name, "BL060-c1-LR3R.b.ab1") self.assertEqual(record.contigs[1].bs[107].padded_start, 2286) self.assertEqual(record.contigs[1].bs[107].padded_end, 2292) self.assertEqual(record.contigs[1].bs[213].name, "BL060c2-LR0R.b.ab1") self.assertEqual(record.contigs[1].bs[213].padded_start, 3236) self.assertEqual(record.contigs[1].bs[213].padded_end, 3296) self.assertEqual(len(record.contigs[1].ct), 1) self.assertEqual(record.contigs[1].ct[0].name, "Contig2") self.assertEqual(record.contigs[1].ct[0].tag_type, "repeat") self.assertEqual(record.contigs[1].ct[0].program, "phrap") self.assertEqual(record.contigs[1].ct[0].padded_start, 42) self.assertEqual(record.contigs[1].ct[0].padded_end, 43) self.assertEqual(record.contigs[1].ct[0].date, "123456:765432") self.assertEqual( record.contigs[1].ct[0].info, ["This is the forst line of comment for c2", "and this the second for c2"], ) self.assertEqual(len(record.contigs[1].wa), 1) self.assertEqual(record.contigs[1].wa[0].tag_type, "phrap_params") self.assertEqual(record.contigs[1].wa[0].program, "phrap") self.assertEqual(record.contigs[1].wa[0].date, "040203:114710") self.assertEqual( record.contigs[1].wa[0].info, [ "phrap 304_nuclsu.fasta.screen -new_ace -retain_duplicates", "phrap version 0.990329", ], ) self.assertEqual(len(record.contigs[1].reads), 14) # Read 0 self.assertEqual(record.contigs[1].reads[0].rd.name, "BL060-c1-LR12.g.ab1") self.assertEqual(record.contigs[1].reads[0].rd.padded_bases, 862) self.assertEqual(record.contigs[1].reads[0].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[0].rd.read_tags, 0) center = len(record.contigs[1].reads[0].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[0].rd.sequence[:10], "cacggatgat") self.assertEqual( record.contigs[1].reads[0].rd.sequence[center - 5 : center + 5], "GTTCTCGTTG", ) self.assertEqual(record.contigs[1].reads[0].rd.sequence[-10:], "CGTTTACCcg") self.assertEqual(record.contigs[1].reads[0].qa.qual_clipping_start, 81) self.assertEqual(record.contigs[1].reads[0].qa.qual_clipping_end, 842) self.assertEqual(record.contigs[1].reads[0].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[0].qa.align_clipping_end, 862) self.assertEqual( record.contigs[1].reads[0].ds.chromat_file, "BL060-c1-LR12.g.ab1" ) self.assertEqual( record.contigs[1].reads[0].ds.phd_file, "BL060-c1-LR12.g.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[0].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(record.contigs[1].reads[0].ds.chem, "term") self.assertEqual(record.contigs[1].reads[0].ds.dye, "big") self.assertEqual(record.contigs[1].reads[0].ds.template, "") self.assertEqual(record.contigs[1].reads[0].ds.direction, "") self.assertIsNone(record.contigs[1].reads[0].rt) self.assertIsNone(record.contigs[1].reads[0].wr) # Read 1 self.assertEqual(record.contigs[1].reads[1].rd.name, "BL060-c1-LR11.g.ab1") self.assertEqual(record.contigs[1].reads[1].rd.padded_bases, 880) self.assertEqual(record.contigs[1].reads[1].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[1].rd.read_tags, 0) center = len(record.contigs[1].reads[1].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[1].rd.sequence[:10], "ctttctgacC") self.assertEqual( record.contigs[1].reads[1].rd.sequence[center - 5 : center + 5], "CTGTGGTTTC", ) self.assertEqual(record.contigs[1].reads[1].rd.sequence[-10:], "cggagttacg") self.assertEqual(record.contigs[1].reads[1].qa.qual_clipping_start, 11) self.assertEqual(record.contigs[1].reads[1].qa.qual_clipping_end, 807) self.assertEqual(record.contigs[1].reads[1].qa.align_clipping_start, 8) self.assertEqual(record.contigs[1].reads[1].qa.align_clipping_end, 880) self.assertEqual( record.contigs[1].reads[1].ds.chromat_file, "BL060-c1-LR11.g.ab1" ) self.assertEqual( record.contigs[1].reads[1].ds.phd_file, "BL060-c1-LR11.g.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[1].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(record.contigs[1].reads[1].ds.chem, "term") self.assertEqual(record.contigs[1].reads[1].ds.dye, "big") self.assertEqual(record.contigs[1].reads[1].ds.template, "") self.assertEqual(record.contigs[1].reads[1].ds.direction, "") self.assertEqual(len(record.contigs[1].reads[1].rt), 0) self.assertIsNone(record.contigs[1].reads[1].wr) # Read 2 self.assertEqual(record.contigs[1].reads[2].rd.name, "BL060-c1-LR9.g.ab1") self.assertEqual(record.contigs[1].reads[2].rd.padded_bases, 864) self.assertEqual(record.contigs[1].reads[2].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[2].rd.read_tags, 0) center = len(record.contigs[1].reads[2].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[2].rd.sequence[:10], "cacccaCTTT") self.assertEqual( record.contigs[1].reads[2].rd.sequence[center - 5 : center + 5], "ACCAAACATT", ) self.assertEqual(record.contigs[1].reads[2].rd.sequence[-10:], "GGTAGCACgc") self.assertEqual(record.contigs[1].reads[2].qa.qual_clipping_start, 7) self.assertEqual(record.contigs[1].reads[2].qa.qual_clipping_end, 840) self.assertEqual(record.contigs[1].reads[2].qa.align_clipping_start, 4) self.assertEqual(record.contigs[1].reads[2].qa.align_clipping_end, 864) self.assertEqual( record.contigs[1].reads[2].ds.chromat_file, "BL060-c1-LR9.g.ab1" ) self.assertEqual( record.contigs[1].reads[2].ds.phd_file, "BL060-c1-LR9.g.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[2].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(record.contigs[1].reads[2].ds.chem, "term") self.assertEqual(record.contigs[1].reads[2].ds.dye, "big") self.assertEqual(record.contigs[1].reads[2].ds.template, "") self.assertEqual(record.contigs[1].reads[2].ds.direction, "") self.assertIsNone(record.contigs[1].reads[2].rt) self.assertIsNone(record.contigs[1].reads[2].wr) # Read 3 self.assertEqual(record.contigs[1].reads[3].rd.name, "BL060-c1-LR17R.b.ab1") self.assertEqual(record.contigs[1].reads[3].rd.padded_bases, 863) self.assertEqual(record.contigs[1].reads[3].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[3].rd.read_tags, 0) center = len(record.contigs[1].reads[3].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[3].rd.sequence[:10], "ctaattggcc") self.assertEqual( record.contigs[1].reads[3].rd.sequence[center - 5 : center + 5], "GGAACCTTTC", ) self.assertEqual(record.contigs[1].reads[3].rd.sequence[-10:], "CAACCTgact") self.assertEqual(record.contigs[1].reads[3].qa.qual_clipping_start, 63) self.assertEqual(record.contigs[1].reads[3].qa.qual_clipping_end, 857) self.assertEqual(record.contigs[1].reads[3].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[3].qa.align_clipping_end, 861) self.assertEqual( record.contigs[1].reads[3].ds.chromat_file, "BL060-c1-LR17R.b.ab1" ) self.assertEqual( record.contigs[1].reads[3].ds.phd_file, "BL060-c1-LR17R.b.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[3].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(record.contigs[1].reads[3].ds.chem, "term") self.assertEqual(record.contigs[1].reads[3].ds.dye, "big") self.assertEqual(record.contigs[1].reads[3].ds.template, "") self.assertEqual(record.contigs[1].reads[3].ds.direction, "") self.assertEqual(record.contigs[1].reads[3].rt, []) self.assertIsNone(record.contigs[1].reads[3].wr) # Read 4 self.assertEqual(record.contigs[1].reads[4].rd.name, "BL060-LR8.5.g.ab1") self.assertEqual(record.contigs[1].reads[4].rd.padded_bases, 877) self.assertEqual(record.contigs[1].reads[4].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[4].rd.read_tags, 0) center = len(record.contigs[1].reads[4].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[4].rd.sequence[:10], "tgCTGCGGTT") self.assertEqual( record.contigs[1].reads[4].rd.sequence[center - 5 : center + 5], "GGCAGTTTCA", ) self.assertEqual(record.contigs[1].reads[4].rd.sequence[-10:], "tactcataaa") self.assertEqual(record.contigs[1].reads[4].qa.qual_clipping_start, 13) self.assertEqual(record.contigs[1].reads[4].qa.qual_clipping_end, 729) self.assertEqual(record.contigs[1].reads[4].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[4].qa.align_clipping_end, 877) self.assertEqual( record.contigs[1].reads[4].ds.chromat_file, "BL060-LR8.5.g.ab1" ) self.assertEqual( record.contigs[1].reads[4].ds.phd_file, "BL060-LR8.5.g.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[4].ds.time, "Fri Nov 14 09:46:03 2003") self.assertEqual(record.contigs[1].reads[4].ds.chem, "term") self.assertEqual(record.contigs[1].reads[4].ds.dye, "big") self.assertEqual(record.contigs[1].reads[4].ds.template, "") self.assertEqual(record.contigs[1].reads[4].ds.direction, "") self.assertIsNone(record.contigs[1].reads[4].rt) self.assertIsNone(record.contigs[1].reads[4].wr) # Read 5 self.assertEqual(record.contigs[1].reads[5].rd.name, "BL060-LR3R.b.ab1") self.assertEqual(record.contigs[1].reads[5].rd.padded_bases, 874) self.assertEqual(record.contigs[1].reads[5].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[5].rd.read_tags, 0) center = len(record.contigs[1].reads[5].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[5].rd.sequence[:10], "ctCTTAGGAT") self.assertEqual( record.contigs[1].reads[5].rd.sequence[center - 5 : center + 5], "AACTCACATT", ) self.assertEqual(record.contigs[1].reads[5].rd.sequence[-10:], "*CACCCAAac") self.assertEqual(record.contigs[1].reads[5].qa.qual_clipping_start, 65) self.assertEqual(record.contigs[1].reads[5].qa.qual_clipping_end, 874) self.assertEqual(record.contigs[1].reads[5].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[5].qa.align_clipping_end, 874) self.assertEqual(record.contigs[1].reads[5].ds.chromat_file, "BL060-LR3R.b.ab1") self.assertEqual( record.contigs[1].reads[5].ds.phd_file, "BL060-LR3R.b.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[5].ds.time, "Fri Nov 14 09:46:03 2003") self.assertEqual(record.contigs[1].reads[5].ds.chem, "term") self.assertEqual(record.contigs[1].reads[5].ds.dye, "big") self.assertEqual(record.contigs[1].reads[5].ds.template, "") self.assertEqual(record.contigs[1].reads[5].ds.direction, "") self.assertIsNone(record.contigs[1].reads[5].rt) self.assertIsNone(record.contigs[1].reads[5].wr) # Read 6 self.assertEqual(record.contigs[1].reads[6].rd.name, "BL060-c1-LR3R.b.ab1") self.assertEqual(record.contigs[1].reads[6].rd.padded_bases, 864) self.assertEqual(record.contigs[1].reads[6].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[6].rd.read_tags, 0) center = len(record.contigs[1].reads[6].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[6].rd.sequence[:10], "CCaTGTCCAA") self.assertEqual( record.contigs[1].reads[6].rd.sequence[center - 5 : center + 5], "AAGGGTT*CA", ) self.assertEqual(record.contigs[1].reads[6].rd.sequence[-10:], "ACACTCGCga") self.assertEqual(record.contigs[1].reads[6].qa.qual_clipping_start, 73) self.assertEqual(record.contigs[1].reads[6].qa.qual_clipping_end, 862) self.assertEqual(record.contigs[1].reads[6].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[6].qa.align_clipping_end, 863) self.assertEqual( record.contigs[1].reads[6].ds.chromat_file, "BL060-c1-LR3R.b.ab1" ) self.assertEqual( record.contigs[1].reads[6].ds.phd_file, "BL060-c1-LR3R.b.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[6].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(record.contigs[1].reads[6].ds.chem, "term") self.assertEqual(record.contigs[1].reads[6].ds.dye, "big") self.assertEqual(record.contigs[1].reads[6].ds.template, "") self.assertEqual(record.contigs[1].reads[6].ds.direction, "") self.assertIsNone(record.contigs[1].reads[6].rt) self.assertIsNone(record.contigs[1].reads[6].wr) # Read 7 self.assertEqual(record.contigs[1].reads[7].rd.name, "BL060-LR3R.b.ab1") self.assertEqual(record.contigs[1].reads[7].rd.padded_bases, 857) self.assertEqual(record.contigs[1].reads[7].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[7].rd.read_tags, 0) center = len(record.contigs[1].reads[7].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[7].rd.sequence[:10], "agaaagagga") self.assertEqual( record.contigs[1].reads[7].rd.sequence[center - 5 : center + 5], "nnnannnnnn", ) self.assertEqual(record.contigs[1].reads[7].rd.sequence[-10:], "gtctttgctc") self.assertEqual(record.contigs[1].reads[7].qa.qual_clipping_start, 548) self.assertEqual(record.contigs[1].reads[7].qa.qual_clipping_end, 847) self.assertEqual(record.contigs[1].reads[7].qa.align_clipping_start, 442) self.assertEqual(record.contigs[1].reads[7].qa.align_clipping_end, 854) self.assertEqual(record.contigs[1].reads[7].ds.chromat_file, "BL060-LR3R.b.ab1") self.assertEqual( record.contigs[1].reads[7].ds.phd_file, "BL060-LR3R.b.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[7].ds.time, "Fri Jan 16 09:01:10 2004") self.assertEqual(record.contigs[1].reads[7].ds.chem, "term") self.assertEqual(record.contigs[1].reads[7].ds.dye, "big") self.assertEqual(record.contigs[1].reads[7].ds.template, "") self.assertEqual(record.contigs[1].reads[7].ds.direction, "") self.assertIsNone(record.contigs[1].reads[7].rt) self.assertIsNone(record.contigs[1].reads[7].wr) # Read 8 self.assertEqual(record.contigs[1].reads[8].rd.name, "BL060-c1-LR7.g.ab1") self.assertEqual(record.contigs[1].reads[8].rd.padded_bases, 878) self.assertEqual(record.contigs[1].reads[8].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[8].rd.read_tags, 0) center = len(record.contigs[1].reads[8].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[8].rd.sequence[:10], "agTttc*ctc") self.assertEqual( record.contigs[1].reads[8].rd.sequence[center - 5 : center + 5], "TCATAAAACT", ) self.assertEqual(record.contigs[1].reads[8].rd.sequence[-10:], "xxxxxxxxxx") self.assertEqual(record.contigs[1].reads[8].qa.qual_clipping_start, 20) self.assertEqual(record.contigs[1].reads[8].qa.qual_clipping_end, 798) self.assertEqual(record.contigs[1].reads[8].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[8].qa.align_clipping_end, 798) self.assertEqual( record.contigs[1].reads[8].ds.chromat_file, "BL060-c1-LR7.g.ab1" ) self.assertEqual( record.contigs[1].reads[8].ds.phd_file, "BL060-c1-LR7.g.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[8].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(record.contigs[1].reads[8].ds.chem, "term") self.assertEqual(record.contigs[1].reads[8].ds.dye, "big") self.assertEqual(record.contigs[1].reads[8].ds.template, "") self.assertEqual(record.contigs[1].reads[8].ds.direction, "") self.assertIsNone(record.contigs[1].reads[8].rt) self.assertIsNone(record.contigs[1].reads[8].wr) # Read 9 self.assertEqual(record.contigs[1].reads[9].rd.name, "BL060-LR7.g.ab1") self.assertEqual(record.contigs[1].reads[9].rd.padded_bases, 880) self.assertEqual(record.contigs[1].reads[9].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[9].rd.read_tags, 0) center = len(record.contigs[1].reads[9].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[9].rd.sequence[:10], "ggctaCGCCc") self.assertEqual( record.contigs[1].reads[9].rd.sequence[center - 5 : center + 5], "ATTGAGTTTC", ) self.assertEqual(record.contigs[1].reads[9].rd.sequence[-10:], "tggcgttgcg") self.assertEqual(record.contigs[1].reads[9].qa.qual_clipping_start, 14) self.assertEqual(record.contigs[1].reads[9].qa.qual_clipping_end, 765) self.assertEqual(record.contigs[1].reads[9].qa.align_clipping_start, 4) self.assertEqual(record.contigs[1].reads[9].qa.align_clipping_end, 765) self.assertEqual(record.contigs[1].reads[9].ds.chromat_file, "BL060-LR7.g.ab1") self.assertEqual( record.contigs[1].reads[9].ds.phd_file, "BL060-LR7.g.ab1.phd.1" ) self.assertEqual(record.contigs[1].reads[9].ds.time, "Fri Nov 14 09:46:03 2003") self.assertEqual(record.contigs[1].reads[9].ds.chem, "term") self.assertEqual(record.contigs[1].reads[9].ds.dye, "big") self.assertEqual(record.contigs[1].reads[9].ds.template, "") self.assertEqual(record.contigs[1].reads[9].ds.direction, "") self.assertIsNone(record.contigs[1].reads[9].rt) self.assertIsNone(record.contigs[1].reads[9].wr) # Read 10 self.assertEqual(record.contigs[1].reads[10].rd.name, "BL060c5-LR5.g.ab1") self.assertEqual(record.contigs[1].reads[10].rd.padded_bases, 871) self.assertEqual(record.contigs[1].reads[10].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[10].rd.read_tags, 0) center = len(record.contigs[1].reads[10].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[10].rd.sequence[:10], "ggtTCGATTA") self.assertEqual( record.contigs[1].reads[10].rd.sequence[center - 5 : center + 5], "ACCAATTGAC", ) self.assertEqual(record.contigs[1].reads[10].rd.sequence[-10:], "ACCACCCatt") self.assertEqual(record.contigs[1].reads[10].qa.qual_clipping_start, 12) self.assertEqual(record.contigs[1].reads[10].qa.qual_clipping_end, 767) self.assertEqual(record.contigs[1].reads[10].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[10].qa.align_clipping_end, 871) self.assertEqual( record.contigs[1].reads[10].ds.chromat_file, "BL060c5-LR5.g.ab1" ) self.assertEqual( record.contigs[1].reads[10].ds.phd_file, "BL060c5-LR5.g.ab1.phd.1" ) self.assertEqual( record.contigs[1].reads[10].ds.time, "Fri Nov 14 09:46:03 2003" ) self.assertEqual(record.contigs[1].reads[10].ds.chem, "term") self.assertEqual(record.contigs[1].reads[10].ds.dye, "big") self.assertEqual(record.contigs[1].reads[10].ds.template, "") self.assertEqual(record.contigs[1].reads[10].ds.direction, "") self.assertIsNone(record.contigs[1].reads[10].rt) self.assertIsNone(record.contigs[1].reads[10].wr) # Read 11 self.assertEqual(record.contigs[1].reads[11].rd.name, "BL060c2-LR5.g.ab1") self.assertEqual(record.contigs[1].reads[11].rd.padded_bases, 839) self.assertEqual(record.contigs[1].reads[11].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[11].rd.read_tags, 0) center = len(record.contigs[1].reads[11].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[11].rd.sequence[:10], "ggttcatatg") self.assertEqual( record.contigs[1].reads[11].rd.sequence[center - 5 : center + 5], "TAAAATCAGT", ) self.assertEqual(record.contigs[1].reads[11].rd.sequence[-10:], "TCTTGCaata") self.assertEqual(record.contigs[1].reads[11].qa.qual_clipping_start, 11) self.assertEqual(record.contigs[1].reads[11].qa.qual_clipping_end, 757) self.assertEqual(record.contigs[1].reads[11].qa.align_clipping_start, 10) self.assertEqual(record.contigs[1].reads[11].qa.align_clipping_end, 835) self.assertIsNone(record.contigs[1].reads[11].ds) self.assertEqual(len(record.contigs[1].reads[11].rt), 1) self.assertEqual(record.contigs[1].reads[11].rt[0].name, "BL060c2-LR5.g.ab1") self.assertEqual( record.contigs[1].reads[11].rt[0].tag_type, "matchElsewhereHighQual" ) self.assertEqual(record.contigs[1].reads[11].rt[0].program, "phrap") self.assertEqual(record.contigs[1].reads[11].rt[0].padded_start, 617) self.assertEqual(record.contigs[1].reads[11].rt[0].padded_end, 631) self.assertEqual(record.contigs[1].reads[11].rt[0].date, "040217:110357") self.assertIsNone(record.contigs[1].reads[11].wr) # Read 12 self.assertEqual(record.contigs[1].reads[12].rd.name, "BL060c5-LR0R.b.ab1") self.assertEqual(record.contigs[1].reads[12].rd.padded_bases, 855) self.assertEqual(record.contigs[1].reads[12].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[12].rd.read_tags, 0) center = len(record.contigs[1].reads[12].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[12].rd.sequence[:10], "cACTCGCGTA") self.assertEqual( record.contigs[1].reads[12].rd.sequence[center - 5 : center + 5], "CTCGTAAAAT", ) self.assertEqual(record.contigs[1].reads[12].rd.sequence[-10:], "aacccctgca") self.assertEqual(record.contigs[1].reads[12].qa.qual_clipping_start, 94) self.assertEqual(record.contigs[1].reads[12].qa.qual_clipping_end, 835) self.assertEqual(record.contigs[1].reads[12].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[12].qa.align_clipping_end, 847) self.assertEqual( record.contigs[1].reads[12].ds.chromat_file, "BL060c5-LR0R.b.ab1" ) self.assertEqual( record.contigs[1].reads[12].ds.phd_file, "BL060c5-LR0R.b.ab1.phd.1" ) self.assertEqual( record.contigs[1].reads[12].ds.time, "Wed Nov 12 08:16:30 2003" ) self.assertEqual(record.contigs[1].reads[12].ds.chem, "term") self.assertEqual(record.contigs[1].reads[12].ds.dye, "big") self.assertEqual(record.contigs[1].reads[12].ds.template, "") self.assertEqual(record.contigs[1].reads[12].ds.direction, "") self.assertEqual(len(record.contigs[1].reads[12].rt), 1) self.assertEqual(record.contigs[1].reads[12].rt[0].name, "BL060c5-LR0R.b.ab1") self.assertEqual( record.contigs[1].reads[12].rt[0].tag_type, "matchElsewhereHighQual" ) self.assertEqual(record.contigs[1].reads[12].rt[0].program, "phrap") self.assertEqual(record.contigs[1].reads[12].rt[0].padded_start, 617) self.assertEqual(record.contigs[1].reads[12].rt[0].padded_end, 631) self.assertEqual(record.contigs[1].reads[12].rt[0].date, "040217:110357") self.assertIsNone(record.contigs[1].reads[12].wr) # Read 13 self.assertEqual(record.contigs[1].reads[13].rd.name, "BL060c2-LR0R.b.ab1") self.assertEqual(record.contigs[1].reads[13].rd.padded_bases, 852) self.assertEqual(record.contigs[1].reads[13].rd.info_items, 0) self.assertEqual(record.contigs[1].reads[13].rd.read_tags, 0) center = len(record.contigs[1].reads[13].rd.sequence) // 2 self.assertEqual(record.contigs[1].reads[13].rd.sequence[:10], "cgCGTa*tTG") self.assertEqual( record.contigs[1].reads[13].rd.sequence[center - 5 : center + 5], "GTAAAATATT", ) self.assertEqual(record.contigs[1].reads[13].rd.sequence[-10:], "Atccttgtag") self.assertEqual(record.contigs[1].reads[13].qa.qual_clipping_start, 33) self.assertEqual(record.contigs[1].reads[13].qa.qual_clipping_end, 831) self.assertEqual(record.contigs[1].reads[13].qa.align_clipping_start, 1) self.assertEqual(record.contigs[1].reads[13].qa.align_clipping_end, 852) self.assertEqual( record.contigs[1].reads[13].ds.chromat_file, "BL060c2-LR0R.b.ab1" ) self.assertEqual( record.contigs[1].reads[13].ds.phd_file, "BL060c2-LR0R.b.ab1.phd.1" ) self.assertEqual( record.contigs[1].reads[13].ds.time, "Wed Nov 12 08:16:29 2003" ) self.assertEqual(record.contigs[1].reads[13].ds.chem, "term") self.assertEqual(record.contigs[1].reads[13].ds.dye, "big") self.assertEqual(record.contigs[1].reads[13].ds.template, "") self.assertEqual(record.contigs[1].reads[13].ds.direction, "") self.assertEqual(record.contigs[1].reads[13].rt, []) self.assertEqual(len(record.contigs[1].reads[13].wr), 1) self.assertEqual(record.contigs[1].reads[13].wr[0].name, "BL060c2-LR0R.b.ab1") self.assertEqual(record.contigs[1].reads[13].wr[0].aligned, "unaligned") self.assertEqual(record.contigs[1].reads[13].wr[0].program, "phrap") self.assertEqual(record.contigs[1].reads[13].wr[0].date, "040217:110357") def test_check_record_parser(self): """Test to check that contig parser parses each contig into a contig.""" contigs = Ace.parse(self.handle) # First contig contig = next(contigs) self.assertEqual(len(contig.reads), 2) self.assertEqual(contig.name, "Contig1") self.assertEqual(contig.nbases, 856) self.assertEqual(contig.nreads, 2) self.assertEqual(contig.nsegments, 31) self.assertEqual(contig.uorc, "U") center = len(contig.sequence) // 2 self.assertEqual(contig.sequence[:10], "aatacgGGAT") self.assertEqual(contig.sequence[center - 5 : center + 5], "ACATCATCTG") self.assertEqual(contig.sequence[-10:], "cATCTAGtac") center = len(contig.quality) // 2 self.assertEqual(contig.quality[:10], [0, 0, 0, 0, 0, 0, 22, 23, 25, 28]) self.assertEqual( contig.quality[center - 5 : center + 5], [90, 90, 90, 90, 90, 90, 90, 90, 90, 90], ) self.assertEqual(contig.quality[-10:], [15, 22, 30, 24, 28, 22, 21, 15, 19, 0]) self.assertEqual(len(contig.af), 2) self.assertEqual(contig.af[1].name, "BL060c3-LR0R.b.ab1") self.assertEqual(contig.af[1].coru, "U") self.assertEqual(contig.af[1].padded_start, 1) self.assertEqual(len(contig.bs), 31) self.assertEqual(contig.bs[15].name, "BL060c3-LR5.g.ab1") self.assertEqual(contig.bs[15].padded_start, 434) self.assertEqual(contig.bs[15].padded_end, 438) self.assertEqual(contig.bs[30].name, "BL060c3-LR0R.b.ab1") self.assertEqual(contig.bs[30].padded_start, 823) self.assertEqual(contig.bs[30].padded_end, 856) self.assertIsNone(contig.ct) self.assertIsNone(contig.wa) self.assertEqual(len(contig.reads), 2) self.assertEqual(contig.reads[0].rd.name, "BL060c3-LR5.g.ab1") self.assertEqual(contig.reads[0].rd.padded_bases, 868) self.assertEqual(contig.reads[0].rd.info_items, 0) self.assertEqual(contig.reads[0].rd.read_tags, 0) center = len(contig.reads[0].rd.sequence) // 2 self.assertEqual(contig.reads[0].rd.sequence[:10], "tagcgaggaa") self.assertEqual( contig.reads[0].rd.sequence[center - 5 : center + 5], "CCGAGGCCAA" ) self.assertEqual(contig.reads[0].rd.sequence[-10:], "gaaccatcag") self.assertEqual(contig.reads[0].qa.qual_clipping_start, 80) self.assertEqual(contig.reads[0].qa.qual_clipping_end, 853) self.assertEqual(contig.reads[0].qa.align_clipping_start, 22) self.assertEqual(contig.reads[0].qa.align_clipping_end, 856) self.assertIsNone(contig.reads[0].ds) self.assertEqual(len(contig.reads[0].rt), 2) self.assertEqual(contig.reads[0].rt[0].name, "BL060c3-LR5.g.ab1") self.assertEqual(contig.reads[0].rt[0].tag_type, "matchElsewhereHighQual") self.assertEqual(contig.reads[0].rt[0].program, "phrap") self.assertEqual(contig.reads[0].rt[0].padded_start, 590) self.assertEqual(contig.reads[0].rt[0].padded_end, 607) self.assertEqual(contig.reads[0].rt[0].date, "040217:110357") self.assertEqual(contig.reads[0].rt[1].name, "BL060c3-LR5.g.ab1") self.assertEqual(contig.reads[0].rt[1].tag_type, "matchElsewhereHighQual") self.assertEqual(contig.reads[0].rt[1].program, "phrap") self.assertEqual(contig.reads[0].rt[1].padded_start, 617) self.assertEqual(contig.reads[0].rt[1].padded_end, 631) self.assertEqual(contig.reads[0].rt[1].date, "040217:110357") self.assertEqual(len(contig.reads[0].wr), 1) self.assertEqual(contig.reads[0].wr[0].name, "BL060c3-LR5.g.ab1") self.assertEqual(contig.reads[0].wr[0].aligned, "unaligned") self.assertEqual(contig.reads[0].wr[0].program, "phrap") self.assertEqual(contig.reads[0].wr[0].date, "040217:110357") self.assertEqual(contig.reads[1].rd.name, "BL060c3-LR0R.b.ab1") self.assertEqual(contig.reads[1].rd.padded_bases, 856) self.assertEqual(contig.reads[1].rd.info_items, 0) self.assertEqual(contig.reads[1].rd.read_tags, 0) center = len(contig.reads[1].rd.sequence) // 2 self.assertEqual(contig.reads[1].rd.sequence[:10], "aatacgGGAT") self.assertEqual( contig.reads[1].rd.sequence[center - 5 : center + 5], "ACATCATCTG" ) self.assertEqual(contig.reads[1].rd.sequence[-10:], "cATCTAGtac") self.assertEqual(contig.reads[1].qa.qual_clipping_start, 7) self.assertEqual(contig.reads[1].qa.qual_clipping_end, 778) self.assertEqual(contig.reads[1].qa.align_clipping_start, 1) self.assertEqual(contig.reads[1].qa.align_clipping_end, 856) self.assertIsNone(contig.reads[1].ds) self.assertIsNone(contig.reads[1].rt) self.assertIsNone(contig.reads[1].wr) # Second contig contig = next(contigs) self.assertEqual(len(contig.reads), 14) self.assertEqual(contig.name, "Contig2") self.assertEqual(contig.nbases, 3296) self.assertEqual(contig.nreads, 14) self.assertEqual(contig.nsegments, 214) self.assertEqual(contig.uorc, "U") center = len(contig.sequence) // 2 self.assertEqual(contig.sequence[:10], "cacggatgat") self.assertEqual(contig.sequence[center - 5 : center + 5], "TTTGAATATT") self.assertEqual(contig.sequence[-10:], "Atccttgtag") center = len(contig.quality) // 2 self.assertEqual(contig.quality[:10], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) self.assertEqual( contig.quality[center - 5 : center + 5], [90, 90, 90, 90, 90, 90, 90, 90, 90, 90], ) self.assertEqual(contig.quality[-10:], [24, 0, 0, 0, 0, 0, 0, 0, 0, 0]) self.assertEqual(len(contig.af), 14) self.assertEqual(contig.af[7].name, "BL060-LR3R.b.ab1") self.assertEqual(contig.af[7].coru, "C") self.assertEqual(contig.af[7].padded_start, 1601) self.assertEqual(contig.af[13].name, "BL060c2-LR0R.b.ab1") self.assertEqual(contig.af[13].coru, "C") self.assertEqual(contig.af[13].padded_start, 2445) self.assertEqual(len(contig.bs), 214) self.assertEqual(contig.bs[107].name, "BL060-c1-LR3R.b.ab1") self.assertEqual(contig.bs[107].padded_start, 2286) self.assertEqual(contig.bs[107].padded_end, 2292) self.assertEqual(contig.bs[213].name, "BL060c2-LR0R.b.ab1") self.assertEqual(contig.bs[213].padded_start, 3236) self.assertEqual(contig.bs[213].padded_end, 3296) self.assertEqual(len(contig.ct), 3) self.assertEqual(contig.ct[0].name, "Contig2") self.assertEqual(contig.ct[0].tag_type, "repeat") self.assertEqual(contig.ct[0].program, "phrap") self.assertEqual(contig.ct[0].padded_start, 42) self.assertEqual(contig.ct[0].padded_end, 43) self.assertEqual(contig.ct[0].date, "123456:765432") self.assertEqual( contig.ct[0].info, ["This is the forst line of comment for c2", "and this the second for c2"], ) self.assertEqual(contig.ct[1].name, "unrelated_Contig") self.assertEqual(contig.ct[1].tag_type, "repeat") self.assertEqual(contig.ct[1].program, "phrap") self.assertEqual(contig.ct[1].padded_start, 1142) self.assertEqual(contig.ct[1].padded_end, 143) self.assertEqual(contig.ct[1].date, "122226:722232") self.assertEqual( contig.ct[1].info, [ "This is the forst line of comment for the unrelated ct tag", "and this the second", ], ) self.assertEqual(contig.ct[2].name, "Contig1") self.assertEqual(contig.ct[2].tag_type, "repeat") self.assertEqual(contig.ct[2].program, "phrap") self.assertEqual(contig.ct[2].padded_start, 52) self.assertEqual(contig.ct[2].padded_end, 53) self.assertEqual(contig.ct[2].date, "555456:555432") self.assertEqual( contig.ct[2].info, ["This is the forst line of comment for c1", "and this the second for c1"], ) self.assertEqual(len(contig.wa), 1) self.assertEqual(contig.wa[0].tag_type, "phrap_params") self.assertEqual(contig.wa[0].program, "phrap") self.assertEqual(contig.wa[0].date, "040203:114710") self.assertEqual( contig.wa[0].info, [ "phrap 304_nuclsu.fasta.screen -new_ace -retain_duplicates", "phrap version 0.990329", ], ) self.assertEqual(len(contig.reads), 14) # Read 0 self.assertEqual(contig.reads[0].rd.name, "BL060-c1-LR12.g.ab1") self.assertEqual(contig.reads[0].rd.padded_bases, 862) self.assertEqual(contig.reads[0].rd.info_items, 0) self.assertEqual(contig.reads[0].rd.read_tags, 0) center = len(contig.reads[0].rd.sequence) // 2 self.assertEqual(contig.reads[0].rd.sequence[:10], "cacggatgat") self.assertEqual( contig.reads[0].rd.sequence[center - 5 : center + 5], "GTTCTCGTTG" ) self.assertEqual(contig.reads[0].rd.sequence[-10:], "CGTTTACCcg") self.assertEqual(contig.reads[0].qa.qual_clipping_start, 81) self.assertEqual(contig.reads[0].qa.qual_clipping_end, 842) self.assertEqual(contig.reads[0].qa.align_clipping_start, 1) self.assertEqual(contig.reads[0].qa.align_clipping_end, 862) self.assertEqual(contig.reads[0].ds.chromat_file, "BL060-c1-LR12.g.ab1") self.assertEqual(contig.reads[0].ds.phd_file, "BL060-c1-LR12.g.ab1.phd.1") self.assertEqual(contig.reads[0].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(contig.reads[0].ds.chem, "term") self.assertEqual(contig.reads[0].ds.dye, "big") self.assertEqual(contig.reads[0].ds.template, "") self.assertEqual(contig.reads[0].ds.direction, "") self.assertIsNone(contig.reads[0].rt) self.assertIsNone(contig.reads[0].wr) # Read 1 self.assertEqual(contig.reads[1].rd.name, "BL060-c1-LR11.g.ab1") self.assertEqual(contig.reads[1].rd.padded_bases, 880) self.assertEqual(contig.reads[1].rd.info_items, 0) self.assertEqual(contig.reads[1].rd.read_tags, 0) center = len(contig.reads[1].rd.sequence) // 2 self.assertEqual(contig.reads[1].rd.sequence[:10], "ctttctgacC") self.assertEqual( contig.reads[1].rd.sequence[center - 5 : center + 5], "CTGTGGTTTC" ) self.assertEqual(contig.reads[1].rd.sequence[-10:], "cggagttacg") self.assertEqual(contig.reads[1].qa.qual_clipping_start, 11) self.assertEqual(contig.reads[1].qa.qual_clipping_end, 807) self.assertEqual(contig.reads[1].qa.align_clipping_start, 8) self.assertEqual(contig.reads[1].qa.align_clipping_end, 880) self.assertEqual(contig.reads[1].ds.chromat_file, "BL060-c1-LR11.g.ab1") self.assertEqual(contig.reads[1].ds.phd_file, "BL060-c1-LR11.g.ab1.phd.1") self.assertEqual(contig.reads[1].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(contig.reads[1].ds.chem, "term") self.assertEqual(contig.reads[1].ds.dye, "big") self.assertEqual(contig.reads[1].ds.template, "") self.assertEqual(contig.reads[1].ds.direction, "") self.assertEqual(len(contig.reads[1].rt), 1) self.assertEqual(contig.reads[1].rt[0].name, "BL060c3-LR5.g.ab1") self.assertEqual(contig.reads[1].rt[0].tag_type, "matchElsewhereHighQual") self.assertEqual(contig.reads[1].rt[0].program, "phrap") self.assertEqual(contig.reads[1].rt[0].padded_start, 617) self.assertEqual(contig.reads[1].rt[0].padded_end, 631) self.assertEqual(contig.reads[1].rt[0].date, "040217:110357") self.assertIsNone(contig.reads[1].wr) # Read 2 self.assertEqual(contig.reads[2].rd.name, "BL060-c1-LR9.g.ab1") self.assertEqual(contig.reads[2].rd.padded_bases, 864) self.assertEqual(contig.reads[2].rd.info_items, 0) self.assertEqual(contig.reads[2].rd.read_tags, 0) center = len(contig.reads[2].rd.sequence) // 2 self.assertEqual(contig.reads[2].rd.sequence[:10], "cacccaCTTT") self.assertEqual( contig.reads[2].rd.sequence[center - 5 : center + 5], "ACCAAACATT" ) self.assertEqual(contig.reads[2].rd.sequence[-10:], "GGTAGCACgc") self.assertEqual(contig.reads[2].qa.qual_clipping_start, 7) self.assertEqual(contig.reads[2].qa.qual_clipping_end, 840) self.assertEqual(contig.reads[2].qa.align_clipping_start, 4) self.assertEqual(contig.reads[2].qa.align_clipping_end, 864) self.assertEqual(contig.reads[2].ds.chromat_file, "BL060-c1-LR9.g.ab1") self.assertEqual(contig.reads[2].ds.phd_file, "BL060-c1-LR9.g.ab1.phd.1") self.assertEqual(contig.reads[2].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(contig.reads[2].ds.chem, "term") self.assertEqual(contig.reads[2].ds.dye, "big") self.assertEqual(contig.reads[2].ds.template, "") self.assertEqual(contig.reads[2].ds.direction, "") self.assertIsNone(contig.reads[2].rt) self.assertIsNone(contig.reads[2].wr) # Read 3 self.assertEqual(contig.reads[3].rd.name, "BL060-c1-LR17R.b.ab1") self.assertEqual(contig.reads[3].rd.padded_bases, 863) self.assertEqual(contig.reads[3].rd.info_items, 0) self.assertEqual(contig.reads[3].rd.read_tags, 0) center = len(contig.reads[3].rd.sequence) // 2 self.assertEqual(contig.reads[3].rd.sequence[:10], "ctaattggcc") self.assertEqual( contig.reads[3].rd.sequence[center - 5 : center + 5], "GGAACCTTTC" ) self.assertEqual(contig.reads[3].rd.sequence[-10:], "CAACCTgact") self.assertEqual(contig.reads[3].qa.qual_clipping_start, 63) self.assertEqual(contig.reads[3].qa.qual_clipping_end, 857) self.assertEqual(contig.reads[3].qa.align_clipping_start, 1) self.assertEqual(contig.reads[3].qa.align_clipping_end, 861) self.assertEqual(contig.reads[3].ds.chromat_file, "BL060-c1-LR17R.b.ab1") self.assertEqual(contig.reads[3].ds.phd_file, "BL060-c1-LR17R.b.ab1.phd.1") self.assertEqual(contig.reads[3].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(contig.reads[3].ds.chem, "term") self.assertEqual(contig.reads[3].ds.dye, "big") self.assertEqual(contig.reads[3].ds.template, "") self.assertEqual(contig.reads[3].ds.direction, "") self.assertEqual(len(contig.reads[3].rt), 1) self.assertEqual(contig.reads[3].rt[0].name, "BL060c3-LR5.g.ab1") self.assertEqual(contig.reads[3].rt[0].tag_type, "matchElsewhereHighQual") self.assertEqual(contig.reads[3].rt[0].program, "phrap") self.assertEqual(contig.reads[3].rt[0].padded_start, 617) self.assertEqual(contig.reads[3].rt[0].padded_end, 631) self.assertEqual(contig.reads[3].rt[0].date, "040217:110357") self.assertIsNone(contig.reads[3].wr) # Read 4 self.assertEqual(contig.reads[4].rd.name, "BL060-LR8.5.g.ab1") self.assertEqual(contig.reads[4].rd.padded_bases, 877) self.assertEqual(contig.reads[4].rd.info_items, 0) self.assertEqual(contig.reads[4].rd.read_tags, 0) center = len(contig.reads[4].rd.sequence) // 2 self.assertEqual(contig.reads[4].rd.sequence[:10], "tgCTGCGGTT") self.assertEqual( contig.reads[4].rd.sequence[center - 5 : center + 5], "GGCAGTTTCA" ) self.assertEqual(contig.reads[4].rd.sequence[-10:], "tactcataaa") self.assertEqual(contig.reads[4].qa.qual_clipping_start, 13) self.assertEqual(contig.reads[4].qa.qual_clipping_end, 729) self.assertEqual(contig.reads[4].qa.align_clipping_start, 1) self.assertEqual(contig.reads[4].qa.align_clipping_end, 877) self.assertEqual(contig.reads[4].ds.chromat_file, "BL060-LR8.5.g.ab1") self.assertEqual(contig.reads[4].ds.phd_file, "BL060-LR8.5.g.ab1.phd.1") self.assertEqual(contig.reads[4].ds.time, "Fri Nov 14 09:46:03 2003") self.assertEqual(contig.reads[4].ds.chem, "term") self.assertEqual(contig.reads[4].ds.dye, "big") self.assertEqual(contig.reads[4].ds.template, "") self.assertEqual(contig.reads[4].ds.direction, "") self.assertIsNone(contig.reads[4].rt) self.assertIsNone(contig.reads[4].wr) # Read 5 self.assertEqual(contig.reads[5].rd.name, "BL060-LR3R.b.ab1") self.assertEqual(contig.reads[5].rd.padded_bases, 874) self.assertEqual(contig.reads[5].rd.info_items, 0) self.assertEqual(contig.reads[5].rd.read_tags, 0) center = len(contig.reads[5].rd.sequence) // 2 self.assertEqual(contig.reads[5].rd.sequence[:10], "ctCTTAGGAT") self.assertEqual( contig.reads[5].rd.sequence[center - 5 : center + 5], "AACTCACATT" ) self.assertEqual(contig.reads[5].rd.sequence[-10:], "*CACCCAAac") self.assertEqual(contig.reads[5].qa.qual_clipping_start, 65) self.assertEqual(contig.reads[5].qa.qual_clipping_end, 874) self.assertEqual(contig.reads[5].qa.align_clipping_start, 1) self.assertEqual(contig.reads[5].qa.align_clipping_end, 874) self.assertEqual(contig.reads[5].ds.chromat_file, "BL060-LR3R.b.ab1") self.assertEqual(contig.reads[5].ds.phd_file, "BL060-LR3R.b.ab1.phd.1") self.assertEqual(contig.reads[5].ds.time, "Fri Nov 14 09:46:03 2003") self.assertEqual(contig.reads[5].ds.chem, "term") self.assertEqual(contig.reads[5].ds.dye, "big") self.assertEqual(contig.reads[5].ds.template, "") self.assertEqual(contig.reads[5].ds.direction, "") self.assertIsNone(contig.reads[5].rt) self.assertIsNone(contig.reads[5].wr) # Read 6 self.assertEqual(contig.reads[6].rd.name, "BL060-c1-LR3R.b.ab1") self.assertEqual(contig.reads[6].rd.padded_bases, 864) self.assertEqual(contig.reads[6].rd.info_items, 0) self.assertEqual(contig.reads[6].rd.read_tags, 0) center = len(contig.reads[6].rd.sequence) // 2 self.assertEqual(contig.reads[6].rd.sequence[:10], "CCaTGTCCAA") self.assertEqual( contig.reads[6].rd.sequence[center - 5 : center + 5], "AAGGGTT*CA" ) self.assertEqual(contig.reads[6].rd.sequence[-10:], "ACACTCGCga") self.assertEqual(contig.reads[6].qa.qual_clipping_start, 73) self.assertEqual(contig.reads[6].qa.qual_clipping_end, 862) self.assertEqual(contig.reads[6].qa.align_clipping_start, 1) self.assertEqual(contig.reads[6].qa.align_clipping_end, 863) self.assertEqual(contig.reads[6].ds.chromat_file, "BL060-c1-LR3R.b.ab1") self.assertEqual(contig.reads[6].ds.phd_file, "BL060-c1-LR3R.b.ab1.phd.1") self.assertEqual(contig.reads[6].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(contig.reads[6].ds.chem, "term") self.assertEqual(contig.reads[6].ds.dye, "big") self.assertEqual(contig.reads[6].ds.template, "") self.assertEqual(contig.reads[6].ds.direction, "") self.assertIsNone(contig.reads[6].rt) self.assertIsNone(contig.reads[6].wr) # Read 7 self.assertEqual(contig.reads[7].rd.name, "BL060-LR3R.b.ab1") self.assertEqual(contig.reads[7].rd.padded_bases, 857) self.assertEqual(contig.reads[7].rd.info_items, 0) self.assertEqual(contig.reads[7].rd.read_tags, 0) center = len(contig.reads[7].rd.sequence) // 2 self.assertEqual(contig.reads[7].rd.sequence[:10], "agaaagagga") self.assertEqual( contig.reads[7].rd.sequence[center - 5 : center + 5], "nnnannnnnn" ) self.assertEqual(contig.reads[7].rd.sequence[-10:], "gtctttgctc") self.assertEqual(contig.reads[7].qa.qual_clipping_start, 548) self.assertEqual(contig.reads[7].qa.qual_clipping_end, 847) self.assertEqual(contig.reads[7].qa.align_clipping_start, 442) self.assertEqual(contig.reads[7].qa.align_clipping_end, 854) self.assertEqual(contig.reads[7].ds.chromat_file, "BL060-LR3R.b.ab1") self.assertEqual(contig.reads[7].ds.phd_file, "BL060-LR3R.b.ab1.phd.1") self.assertEqual(contig.reads[7].ds.time, "Fri Jan 16 09:01:10 2004") self.assertEqual(contig.reads[7].ds.chem, "term") self.assertEqual(contig.reads[7].ds.dye, "big") self.assertEqual(contig.reads[7].ds.template, "") self.assertEqual(contig.reads[7].ds.direction, "") self.assertIsNone(contig.reads[7].rt) self.assertIsNone(contig.reads[7].wr) # Read 8 self.assertEqual(contig.reads[8].rd.name, "BL060-c1-LR7.g.ab1") self.assertEqual(contig.reads[8].rd.padded_bases, 878) self.assertEqual(contig.reads[8].rd.info_items, 0) self.assertEqual(contig.reads[8].rd.read_tags, 0) center = len(contig.reads[8].rd.sequence) // 2 self.assertEqual(contig.reads[8].rd.sequence[:10], "agTttc*ctc") self.assertEqual( contig.reads[8].rd.sequence[center - 5 : center + 5], "TCATAAAACT" ) self.assertEqual(contig.reads[8].rd.sequence[-10:], "xxxxxxxxxx") self.assertEqual(contig.reads[8].qa.qual_clipping_start, 20) self.assertEqual(contig.reads[8].qa.qual_clipping_end, 798) self.assertEqual(contig.reads[8].qa.align_clipping_start, 1) self.assertEqual(contig.reads[8].qa.align_clipping_end, 798) self.assertEqual(contig.reads[8].ds.chromat_file, "BL060-c1-LR7.g.ab1") self.assertEqual(contig.reads[8].ds.phd_file, "BL060-c1-LR7.g.ab1.phd.1") self.assertEqual(contig.reads[8].ds.time, "Tue Feb 3 11:01:16 2004") self.assertEqual(contig.reads[8].ds.chem, "term") self.assertEqual(contig.reads[8].ds.dye, "big") self.assertEqual(contig.reads[8].ds.template, "") self.assertEqual(contig.reads[8].ds.direction, "") self.assertIsNone(contig.reads[8].rt) self.assertIsNone(contig.reads[8].wr) # Read 9 self.assertEqual(contig.reads[9].rd.name, "BL060-LR7.g.ab1") self.assertEqual(contig.reads[9].rd.padded_bases, 880) self.assertEqual(contig.reads[9].rd.info_items, 0) self.assertEqual(contig.reads[9].rd.read_tags, 0) center = len(contig.reads[9].rd.sequence) // 2 self.assertEqual(contig.reads[9].rd.sequence[:10], "ggctaCGCCc") self.assertEqual( contig.reads[9].rd.sequence[center - 5 : center + 5], "ATTGAGTTTC" ) self.assertEqual(contig.reads[9].rd.sequence[-10:], "tggcgttgcg") self.assertEqual(contig.reads[9].qa.qual_clipping_start, 14) self.assertEqual(contig.reads[9].qa.qual_clipping_end, 765) self.assertEqual(contig.reads[9].qa.align_clipping_start, 4) self.assertEqual(contig.reads[9].qa.align_clipping_end, 765) self.assertEqual(contig.reads[9].ds.chromat_file, "BL060-LR7.g.ab1") self.assertEqual(contig.reads[9].ds.phd_file, "BL060-LR7.g.ab1.phd.1") self.assertEqual(contig.reads[9].ds.time, "Fri Nov 14 09:46:03 2003") self.assertEqual(contig.reads[9].ds.chem, "term") self.assertEqual(contig.reads[9].ds.dye, "big") self.assertEqual(contig.reads[9].ds.template, "") self.assertEqual(contig.reads[9].ds.direction, "") self.assertIsNone(contig.reads[9].rt) self.assertIsNone(contig.reads[9].wr) # Read 10 self.assertEqual(contig.reads[10].rd.name, "BL060c5-LR5.g.ab1") self.assertEqual(contig.reads[10].rd.padded_bases, 871) self.assertEqual(contig.reads[10].rd.info_items, 0) self.assertEqual(contig.reads[10].rd.read_tags, 0) center = len(contig.reads[10].rd.sequence) // 2 self.assertEqual(contig.reads[10].rd.sequence[:10], "ggtTCGATTA") self.assertEqual( contig.reads[10].rd.sequence[center - 5 : center + 5], "ACCAATTGAC" ) self.assertEqual(contig.reads[10].rd.sequence[-10:], "ACCACCCatt") self.assertEqual(contig.reads[10].qa.qual_clipping_start, 12) self.assertEqual(contig.reads[10].qa.qual_clipping_end, 767) self.assertEqual(contig.reads[10].qa.align_clipping_start, 1) self.assertEqual(contig.reads[10].qa.align_clipping_end, 871) self.assertEqual(contig.reads[10].ds.chromat_file, "BL060c5-LR5.g.ab1") self.assertEqual(contig.reads[10].ds.phd_file, "BL060c5-LR5.g.ab1.phd.1") self.assertEqual(contig.reads[10].ds.time, "Fri Nov 14 09:46:03 2003") self.assertEqual(contig.reads[10].ds.chem, "term") self.assertEqual(contig.reads[10].ds.dye, "big") self.assertEqual(contig.reads[10].ds.template, "") self.assertEqual(contig.reads[10].ds.direction, "") self.assertIsNone(contig.reads[10].rt) self.assertIsNone(contig.reads[10].wr) # Read 11 self.assertEqual(contig.reads[11].rd.name, "BL060c2-LR5.g.ab1") self.assertEqual(contig.reads[11].rd.padded_bases, 839) self.assertEqual(contig.reads[11].rd.info_items, 0) self.assertEqual(contig.reads[11].rd.read_tags, 0) center = len(contig.reads[11].rd.sequence) // 2 self.assertEqual(contig.reads[11].rd.sequence[:10], "ggttcatatg") self.assertEqual( contig.reads[11].rd.sequence[center - 5 : center + 5], "TAAAATCAGT" ) self.assertEqual(contig.reads[11].rd.sequence[-10:], "TCTTGCaata") self.assertEqual(contig.reads[11].qa.qual_clipping_start, 11) self.assertEqual(contig.reads[11].qa.qual_clipping_end, 757) self.assertEqual(contig.reads[11].qa.align_clipping_start, 10) self.assertEqual(contig.reads[11].qa.align_clipping_end, 835) self.assertIsNone(contig.reads[11].ds) self.assertEqual(len(contig.reads[11].rt), 1) self.assertEqual(contig.reads[11].rt[0].name, "BL060c2-LR5.g.ab1") self.assertEqual(contig.reads[11].rt[0].tag_type, "matchElsewhereHighQual") self.assertEqual(contig.reads[11].rt[0].program, "phrap") self.assertEqual(contig.reads[11].rt[0].padded_start, 617) self.assertEqual(contig.reads[11].rt[0].padded_end, 631) self.assertEqual(contig.reads[11].rt[0].date, "040217:110357") self.assertIsNone(contig.reads[11].wr) # Read 12 self.assertEqual(contig.reads[12].rd.name, "BL060c5-LR0R.b.ab1") self.assertEqual(contig.reads[12].rd.padded_bases, 855) self.assertEqual(contig.reads[12].rd.info_items, 0) self.assertEqual(contig.reads[12].rd.read_tags, 0) center = len(contig.reads[12].rd.sequence) // 2 self.assertEqual(contig.reads[12].rd.sequence[:10], "cACTCGCGTA") self.assertEqual( contig.reads[12].rd.sequence[center - 5 : center + 5], "CTCGTAAAAT" ) self.assertEqual(contig.reads[12].rd.sequence[-10:], "aacccctgca") self.assertEqual(contig.reads[12].qa.qual_clipping_start, 94) self.assertEqual(contig.reads[12].qa.qual_clipping_end, 835) self.assertEqual(contig.reads[12].qa.align_clipping_start, 1) self.assertEqual(contig.reads[12].qa.align_clipping_end, 847) self.assertEqual(contig.reads[12].ds.chromat_file, "BL060c5-LR0R.b.ab1") self.assertEqual(contig.reads[12].ds.phd_file, "BL060c5-LR0R.b.ab1.phd.1") self.assertEqual(contig.reads[12].ds.time, "Wed Nov 12 08:16:30 2003") self.assertEqual(contig.reads[12].ds.chem, "term") self.assertEqual(contig.reads[12].ds.dye, "big") self.assertEqual(contig.reads[12].ds.template, "") self.assertEqual(contig.reads[12].ds.direction, "") self.assertIsNone(contig.reads[12].rt) self.assertIsNone(contig.reads[12].wr) # Read 13 self.assertEqual(contig.reads[13].rd.name, "BL060c2-LR0R.b.ab1") self.assertEqual(contig.reads[13].rd.padded_bases, 852) self.assertEqual(contig.reads[13].rd.info_items, 0) self.assertEqual(contig.reads[13].rd.read_tags, 0) center = len(contig.reads[13].rd.sequence) // 2 self.assertEqual(contig.reads[13].rd.sequence[:10], "cgCGTa*tTG") self.assertEqual( contig.reads[13].rd.sequence[center - 5 : center + 5], "GTAAAATATT" ) self.assertEqual(contig.reads[13].rd.sequence[-10:], "Atccttgtag") self.assertEqual(contig.reads[13].qa.qual_clipping_start, 33) self.assertEqual(contig.reads[13].qa.qual_clipping_end, 831) self.assertEqual(contig.reads[13].qa.align_clipping_start, 1) self.assertEqual(contig.reads[13].qa.align_clipping_end, 852) self.assertEqual(contig.reads[13].ds.chromat_file, "BL060c2-LR0R.b.ab1") self.assertEqual(contig.reads[13].ds.phd_file, "BL060c2-LR0R.b.ab1.phd.1") self.assertEqual(contig.reads[13].ds.time, "Wed Nov 12 08:16:29 2003") self.assertEqual(contig.reads[13].ds.chem, "term") self.assertEqual(contig.reads[13].ds.dye, "big") self.assertEqual(contig.reads[13].ds.template, "") self.assertEqual(contig.reads[13].ds.direction, "") self.assertEqual(len(contig.reads[13].rt), 1) self.assertEqual(contig.reads[13].rt[0].name, "BL060c5-LR0R.b.ab1") self.assertEqual(contig.reads[13].rt[0].tag_type, "matchElsewhereHighQual") self.assertEqual(contig.reads[13].rt[0].program, "phrap") self.assertEqual(contig.reads[13].rt[0].padded_start, 617) self.assertEqual(contig.reads[13].rt[0].padded_end, 631) self.assertEqual(contig.reads[13].rt[0].date, "040217:110357") self.assertEqual(len(contig.reads[13].wr), 1) self.assertEqual(contig.reads[13].wr[0].name, "BL060c2-LR0R.b.ab1") self.assertEqual(contig.reads[13].wr[0].aligned, "unaligned") self.assertEqual(contig.reads[13].wr[0].program, "phrap") self.assertEqual(contig.reads[13].wr[0].date, "040217:110357") # Make sure there are no more contigs self.assertRaises(StopIteration, next, contigs) class AceTestTwo(unittest.TestCase): """Test parsing example output from CAP3. The sample input file seq.cap.ace was downloaded from: http://genome.cs.mtu.edu/cap/data/seq.cap.ace """ def setUp(self): self.handle = open("Ace/seq.cap.ace") def tearDown(self): self.handle.close() def test_check_ACEParser(self): """Test to check that ACEParser can parse the whole file into one record.""" record = Ace.read(self.handle) self.assertEqual(record.ncontigs, 1) self.assertEqual(record.nreads, 6) self.assertIsNone(record.wa) self.assertEqual(len(record.contigs), 1) self.assertEqual(len(record.contigs[0].reads), 6) self.assertEqual(record.contigs[0].name, "Contig1") self.assertEqual(record.contigs[0].nbases, 1222) self.assertEqual(record.contigs[0].nreads, 6) self.assertEqual(record.contigs[0].nsegments, 0) self.assertEqual(record.contigs[0].uorc, "U") center = len(record.contigs[0].sequence) // 2 self.assertEqual(record.contigs[0].sequence[:10], "AGTTTTAGTT") self.assertEqual( record.contigs[0].sequence[center - 5 : center + 5], "TGTGCGCGCA" ) self.assertEqual(record.contigs[0].sequence[-10:], "ATATCACATT") center = len(record.contigs[0].quality) // 2 self.assertEqual( record.contigs[0].quality[:10], [61, 66, 67, 70, 71, 73, 73, 77, 77, 87] ) self.assertEqual( record.contigs[0].quality[center - 5 : center + 5], [97, 97, 97, 97, 97, 97, 97, 97, 97, 97], ) self.assertEqual( record.contigs[0].quality[-10:], [56, 51, 49, 41, 38, 39, 45, 44, 49, 46] ) self.assertEqual(len(record.contigs[0].af), 6) self.assertEqual(len(record.contigs[0].bs), 0) self.assertEqual(record.contigs[0].af[3].name, "R5") self.assertEqual(record.contigs[0].af[3].coru, "C") self.assertEqual(record.contigs[0].af[3].padded_start, 320) self.assertEqual(record.contigs[0].af[5].name, "R6") self.assertEqual(record.contigs[0].af[5].coru, "C") self.assertEqual(record.contigs[0].af[5].padded_start, 517) self.assertEqual(record.contigs[0].bs, []) self.assertIsNone(record.contigs[0].ct) self.assertIsNone(record.contigs[0].wa) self.assertEqual(len(record.contigs[0].reads), 6) self.assertEqual(record.contigs[0].reads[0].rd.name, "R3") self.assertEqual(record.contigs[0].reads[0].rd.padded_bases, 919) self.assertEqual(record.contigs[0].reads[0].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[0].rd.read_tags, 0) center = len(record.contigs[0].reads[0].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[0].rd.sequence[:10], "NNNNNNNNNN") self.assertEqual( record.contigs[0].reads[0].rd.sequence[center - 5 : center + 5], "ATGTGCGCTC", ) self.assertEqual(record.contigs[0].reads[0].rd.sequence[-10:], "CAGCTCACCA") self.assertEqual(record.contigs[0].reads[0].qa.qual_clipping_start, 55) self.assertEqual(record.contigs[0].reads[0].qa.qual_clipping_end, 916) self.assertEqual(record.contigs[0].reads[0].qa.align_clipping_start, 55) self.assertEqual(record.contigs[0].reads[0].qa.align_clipping_end, 916) self.assertEqual(record.contigs[0].reads[0].ds.chromat_file, "") self.assertEqual(record.contigs[0].reads[0].ds.phd_file, "") self.assertEqual(record.contigs[0].reads[0].ds.time, "") self.assertEqual(record.contigs[0].reads[0].ds.chem, "") self.assertEqual(record.contigs[0].reads[0].ds.dye, "") self.assertEqual(record.contigs[0].reads[0].ds.template, "") self.assertEqual(record.contigs[0].reads[0].ds.direction, "") self.assertIsNone(record.contigs[0].reads[0].rt) self.assertIsNone(record.contigs[0].reads[0].wr) self.assertEqual(record.contigs[0].reads[1].rd.name, "R1") self.assertEqual(record.contigs[0].reads[1].rd.padded_bases, 864) self.assertEqual(record.contigs[0].reads[1].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[1].rd.read_tags, 0) center = len(record.contigs[0].reads[1].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[1].rd.sequence[:10], "AGCCGGTACC") self.assertEqual( record.contigs[0].reads[1].rd.sequence[center - 5 : center + 5], "GGGATGGCAC", ) self.assertEqual(record.contigs[0].reads[1].rd.sequence[-10:], "GGGCTGGGAG") self.assertEqual(record.contigs[0].reads[1].qa.qual_clipping_start, 12) self.assertEqual(record.contigs[0].reads[1].qa.qual_clipping_end, 863) self.assertEqual(record.contigs[0].reads[1].qa.align_clipping_start, 12) self.assertEqual(record.contigs[0].reads[1].qa.align_clipping_end, 863) self.assertEqual(record.contigs[0].reads[1].ds.chromat_file, "") self.assertEqual(record.contigs[0].reads[1].ds.phd_file, "") self.assertEqual(record.contigs[0].reads[1].ds.time, "") self.assertEqual(record.contigs[0].reads[1].ds.chem, "") self.assertEqual(record.contigs[0].reads[1].ds.dye, "") self.assertEqual(record.contigs[0].reads[1].ds.template, "") self.assertEqual(record.contigs[0].reads[1].ds.direction, "") self.assertIsNone(record.contigs[0].reads[1].rt) self.assertIsNone(record.contigs[0].reads[1].wr) self.assertEqual(record.contigs[0].reads[2].rd.name, "R2") self.assertEqual(record.contigs[0].reads[2].rd.padded_bases, 1026) self.assertEqual(record.contigs[0].reads[2].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[2].rd.read_tags, 0) center = len(record.contigs[0].reads[2].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[2].rd.sequence[:10], "NNNNNNNNNN") self.assertEqual( record.contigs[0].reads[2].rd.sequence[center - 5 : center + 5], "GGATGCCTGG", ) self.assertEqual(record.contigs[0].reads[2].rd.sequence[-10:], "GGTTGAGGCC") self.assertEqual(record.contigs[0].reads[2].qa.qual_clipping_start, 55) self.assertEqual(record.contigs[0].reads[2].qa.qual_clipping_end, 1000) self.assertEqual(record.contigs[0].reads[2].qa.align_clipping_start, 55) self.assertEqual(record.contigs[0].reads[2].qa.align_clipping_end, 1000) self.assertEqual(record.contigs[0].reads[2].ds.chromat_file, "") self.assertEqual(record.contigs[0].reads[2].ds.phd_file, "") self.assertEqual(record.contigs[0].reads[2].ds.time, "") self.assertEqual(record.contigs[0].reads[2].ds.chem, "") self.assertEqual(record.contigs[0].reads[2].ds.dye, "") self.assertEqual(record.contigs[0].reads[2].ds.template, "") self.assertEqual(record.contigs[0].reads[2].ds.direction, "") self.assertIsNone(record.contigs[0].reads[2].rt) self.assertIsNone(record.contigs[0].reads[2].wr) self.assertEqual(record.contigs[0].reads[3].rd.name, "R5") self.assertEqual(record.contigs[0].reads[3].rd.padded_bases, 925) self.assertEqual(record.contigs[0].reads[3].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[3].rd.read_tags, 0) center = len(record.contigs[0].reads[3].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[3].rd.sequence[:10], "NNNNNNNNNN") self.assertEqual( record.contigs[0].reads[3].rd.sequence[center - 5 : center + 5], "CCTCCCTACA", ) self.assertEqual(record.contigs[0].reads[3].rd.sequence[-10:], "GCCCCCGGNN") self.assertEqual(record.contigs[0].reads[3].qa.qual_clipping_start, 293) self.assertEqual(record.contigs[0].reads[3].qa.qual_clipping_end, 874) self.assertEqual(record.contigs[0].reads[3].qa.align_clipping_start, 293) self.assertEqual(record.contigs[0].reads[3].qa.align_clipping_end, 874) self.assertEqual(record.contigs[0].reads[3].ds.chromat_file, "") self.assertEqual(record.contigs[0].reads[3].ds.phd_file, "") self.assertEqual(record.contigs[0].reads[3].ds.time, "") self.assertEqual(record.contigs[0].reads[3].ds.chem, "") self.assertEqual(record.contigs[0].reads[3].ds.dye, "") self.assertEqual(record.contigs[0].reads[3].ds.template, "") self.assertEqual(record.contigs[0].reads[3].ds.direction, "") self.assertIsNone(record.contigs[0].reads[3].rt) self.assertIsNone(record.contigs[0].reads[3].wr) self.assertEqual(record.contigs[0].reads[4].rd.name, "R4") self.assertEqual(record.contigs[0].reads[4].rd.padded_bases, 816) self.assertEqual(record.contigs[0].reads[4].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[4].rd.read_tags, 0) center = len(record.contigs[0].reads[4].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[4].rd.sequence[:10], "CACTCAGCTC") self.assertEqual( record.contigs[0].reads[4].rd.sequence[center - 5 : center + 5], "TCCAAAGGGT", ) self.assertEqual(record.contigs[0].reads[4].rd.sequence[-10:], "AGCTGAATCG") self.assertEqual(record.contigs[0].reads[4].qa.qual_clipping_start, 1) self.assertEqual(record.contigs[0].reads[4].qa.qual_clipping_end, 799) self.assertEqual(record.contigs[0].reads[4].qa.align_clipping_start, 1) self.assertEqual(record.contigs[0].reads[4].qa.align_clipping_end, 799) self.assertEqual(record.contigs[0].reads[4].ds.chromat_file, "") self.assertEqual(record.contigs[0].reads[4].ds.phd_file, "") self.assertEqual(record.contigs[0].reads[4].ds.time, "") self.assertEqual(record.contigs[0].reads[4].ds.chem, "") self.assertEqual(record.contigs[0].reads[4].ds.dye, "") self.assertEqual(record.contigs[0].reads[4].ds.template, "") self.assertEqual(record.contigs[0].reads[4].ds.direction, "") self.assertIsNone(record.contigs[0].reads[4].rt) self.assertIsNone(record.contigs[0].reads[4].wr) self.assertEqual(record.contigs[0].reads[5].rd.name, "R6") self.assertEqual(record.contigs[0].reads[5].rd.padded_bases, 857) self.assertEqual(record.contigs[0].reads[5].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[5].rd.read_tags, 0) center = len(record.contigs[0].reads[5].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[5].rd.sequence[:10], "CCGGCAGTGA") self.assertEqual( record.contigs[0].reads[5].rd.sequence[center - 5 : center + 5], "AAAAAAAACC", ) self.assertEqual(record.contigs[0].reads[5].rd.sequence[-10:], "NNNNNNNNNN") self.assertEqual(record.contigs[0].reads[5].qa.qual_clipping_start, 24) self.assertEqual(record.contigs[0].reads[5].qa.qual_clipping_end, 706) self.assertEqual(record.contigs[0].reads[5].qa.align_clipping_start, 24) self.assertEqual(record.contigs[0].reads[5].qa.align_clipping_end, 706) self.assertEqual(record.contigs[0].reads[5].ds.chromat_file, "") self.assertEqual(record.contigs[0].reads[5].ds.phd_file, "") self.assertEqual(record.contigs[0].reads[5].ds.time, "") self.assertEqual(record.contigs[0].reads[5].ds.chem, "") self.assertEqual(record.contigs[0].reads[5].ds.dye, "") self.assertEqual(record.contigs[0].reads[5].ds.template, "") self.assertEqual(record.contigs[0].reads[5].ds.direction, "") self.assertIsNone(record.contigs[0].reads[5].rt) self.assertIsNone(record.contigs[0].reads[5].wr) def test_check_record_parser(self): """Test to check that record parser parses each contig into a record.""" contigs = Ace.parse(self.handle) # First (and only) contig contig = next(contigs) self.assertEqual(len(contig.reads), 6) self.assertEqual(contig.name, "Contig1") self.assertEqual(contig.nbases, 1222) self.assertEqual(contig.nreads, 6) self.assertEqual(contig.nsegments, 0) self.assertEqual(contig.uorc, "U") center = len(contig.sequence) // 2 self.assertEqual(contig.sequence[:10], "AGTTTTAGTT") self.assertEqual(contig.sequence[center - 5 : center + 5], "TGTGCGCGCA") self.assertEqual(contig.sequence[-10:], "ATATCACATT") center = len(contig.quality) // 2 self.assertEqual(contig.quality[:10], [61, 66, 67, 70, 71, 73, 73, 77, 77, 87]) self.assertEqual( contig.quality[center - 5 : center + 5], [97, 97, 97, 97, 97, 97, 97, 97, 97, 97], ) self.assertEqual(contig.quality[-10:], [56, 51, 49, 41, 38, 39, 45, 44, 49, 46]) self.assertEqual(len(contig.af), 6) self.assertEqual(len(contig.bs), 0) self.assertEqual(contig.af[3].name, "R5") self.assertEqual(contig.af[3].coru, "C") self.assertEqual(contig.af[3].padded_start, 320) self.assertEqual(contig.af[5].name, "R6") self.assertEqual(contig.af[5].coru, "C") self.assertEqual(contig.af[5].padded_start, 517) self.assertEqual(contig.bs, []) self.assertIsNone(contig.ct) self.assertIsNone(contig.wa) self.assertEqual(len(contig.reads), 6) self.assertEqual(contig.reads[0].rd.name, "R3") self.assertEqual(contig.reads[0].rd.padded_bases, 919) self.assertEqual(contig.reads[0].rd.info_items, 0) self.assertEqual(contig.reads[0].rd.read_tags, 0) center = len(contig.reads[0].rd.sequence) // 2 self.assertEqual(contig.reads[0].rd.sequence[:10], "NNNNNNNNNN") self.assertEqual( contig.reads[0].rd.sequence[center - 5 : center + 5], "ATGTGCGCTC" ) self.assertEqual(contig.reads[0].rd.sequence[-10:], "CAGCTCACCA") self.assertEqual(contig.reads[0].qa.qual_clipping_start, 55) self.assertEqual(contig.reads[0].qa.qual_clipping_end, 916) self.assertEqual(contig.reads[0].qa.align_clipping_start, 55) self.assertEqual(contig.reads[0].qa.align_clipping_end, 916) self.assertEqual(contig.reads[0].ds.chromat_file, "") self.assertEqual(contig.reads[0].ds.phd_file, "") self.assertEqual(contig.reads[0].ds.time, "") self.assertEqual(contig.reads[0].ds.chem, "") self.assertEqual(contig.reads[0].ds.dye, "") self.assertEqual(contig.reads[0].ds.template, "") self.assertEqual(contig.reads[0].ds.direction, "") self.assertIsNone(contig.reads[0].rt) self.assertIsNone(contig.reads[0].wr) self.assertEqual(contig.reads[1].rd.name, "R1") self.assertEqual(contig.reads[1].rd.padded_bases, 864) self.assertEqual(contig.reads[1].rd.info_items, 0) self.assertEqual(contig.reads[1].rd.read_tags, 0) center = len(contig.reads[1].rd.sequence) // 2 self.assertEqual(contig.reads[1].rd.sequence[:10], "AGCCGGTACC") self.assertEqual( contig.reads[1].rd.sequence[center - 5 : center + 5], "GGGATGGCAC" ) self.assertEqual(contig.reads[1].rd.sequence[-10:], "GGGCTGGGAG") self.assertEqual(contig.reads[1].qa.qual_clipping_start, 12) self.assertEqual(contig.reads[1].qa.qual_clipping_end, 863) self.assertEqual(contig.reads[1].qa.align_clipping_start, 12) self.assertEqual(contig.reads[1].qa.align_clipping_end, 863) self.assertEqual(contig.reads[1].ds.chromat_file, "") self.assertEqual(contig.reads[1].ds.phd_file, "") self.assertEqual(contig.reads[1].ds.time, "") self.assertEqual(contig.reads[1].ds.chem, "") self.assertEqual(contig.reads[1].ds.dye, "") self.assertEqual(contig.reads[1].ds.template, "") self.assertEqual(contig.reads[1].ds.direction, "") self.assertIsNone(contig.reads[1].rt) self.assertIsNone(contig.reads[1].wr) self.assertEqual(contig.reads[2].rd.name, "R2") self.assertEqual(contig.reads[2].rd.padded_bases, 1026) self.assertEqual(contig.reads[2].rd.info_items, 0) self.assertEqual(contig.reads[2].rd.read_tags, 0) center = len(contig.reads[2].rd.sequence) // 2 self.assertEqual(contig.reads[2].rd.sequence[:10], "NNNNNNNNNN") self.assertEqual( contig.reads[2].rd.sequence[center - 5 : center + 5], "GGATGCCTGG" ) self.assertEqual(contig.reads[2].rd.sequence[-10:], "GGTTGAGGCC") self.assertEqual(contig.reads[2].qa.qual_clipping_start, 55) self.assertEqual(contig.reads[2].qa.qual_clipping_end, 1000) self.assertEqual(contig.reads[2].qa.align_clipping_start, 55) self.assertEqual(contig.reads[2].qa.align_clipping_end, 1000) self.assertEqual(contig.reads[2].ds.chromat_file, "") self.assertEqual(contig.reads[2].ds.phd_file, "") self.assertEqual(contig.reads[2].ds.time, "") self.assertEqual(contig.reads[2].ds.chem, "") self.assertEqual(contig.reads[2].ds.dye, "") self.assertEqual(contig.reads[2].ds.template, "") self.assertEqual(contig.reads[2].ds.direction, "") self.assertIsNone(contig.reads[2].rt) self.assertIsNone(contig.reads[2].wr) self.assertEqual(contig.reads[3].rd.name, "R5") self.assertEqual(contig.reads[3].rd.padded_bases, 925) self.assertEqual(contig.reads[3].rd.info_items, 0) self.assertEqual(contig.reads[3].rd.read_tags, 0) center = len(contig.reads[3].rd.sequence) // 2 self.assertEqual(contig.reads[3].rd.sequence[:10], "NNNNNNNNNN") self.assertEqual( contig.reads[3].rd.sequence[center - 5 : center + 5], "CCTCCCTACA" ) self.assertEqual(contig.reads[3].rd.sequence[-10:], "GCCCCCGGNN") self.assertEqual(contig.reads[3].qa.qual_clipping_start, 293) self.assertEqual(contig.reads[3].qa.qual_clipping_end, 874) self.assertEqual(contig.reads[3].qa.align_clipping_start, 293) self.assertEqual(contig.reads[3].qa.align_clipping_end, 874) self.assertEqual(contig.reads[3].ds.chromat_file, "") self.assertEqual(contig.reads[3].ds.phd_file, "") self.assertEqual(contig.reads[3].ds.time, "") self.assertEqual(contig.reads[3].ds.chem, "") self.assertEqual(contig.reads[3].ds.dye, "") self.assertEqual(contig.reads[3].ds.template, "") self.assertEqual(contig.reads[3].ds.direction, "") self.assertIsNone(contig.reads[3].rt) self.assertIsNone(contig.reads[3].wr) self.assertEqual(contig.reads[4].rd.name, "R4") self.assertEqual(contig.reads[4].rd.padded_bases, 816) self.assertEqual(contig.reads[4].rd.info_items, 0) self.assertEqual(contig.reads[4].rd.read_tags, 0) center = len(contig.reads[4].rd.sequence) // 2 self.assertEqual(contig.reads[4].rd.sequence[:10], "CACTCAGCTC") self.assertEqual( contig.reads[4].rd.sequence[center - 5 : center + 5], "TCCAAAGGGT" ) self.assertEqual(contig.reads[4].rd.sequence[-10:], "AGCTGAATCG") self.assertEqual(contig.reads[4].qa.qual_clipping_start, 1) self.assertEqual(contig.reads[4].qa.qual_clipping_end, 799) self.assertEqual(contig.reads[4].qa.align_clipping_start, 1) self.assertEqual(contig.reads[4].qa.align_clipping_end, 799) self.assertEqual(contig.reads[4].ds.chromat_file, "") self.assertEqual(contig.reads[4].ds.phd_file, "") self.assertEqual(contig.reads[4].ds.time, "") self.assertEqual(contig.reads[4].ds.chem, "") self.assertEqual(contig.reads[4].ds.dye, "") self.assertEqual(contig.reads[4].ds.template, "") self.assertEqual(contig.reads[4].ds.direction, "") self.assertIsNone(contig.reads[4].rt) self.assertIsNone(contig.reads[4].wr) self.assertEqual(contig.reads[5].rd.name, "R6") self.assertEqual(contig.reads[5].rd.padded_bases, 857) self.assertEqual(contig.reads[5].rd.info_items, 0) self.assertEqual(contig.reads[5].rd.read_tags, 0) center = len(contig.reads[5].rd.sequence) // 2 self.assertEqual(contig.reads[5].rd.sequence[:10], "CCGGCAGTGA") self.assertEqual( contig.reads[5].rd.sequence[center - 5 : center + 5], "AAAAAAAACC" ) self.assertEqual(contig.reads[5].rd.sequence[-10:], "NNNNNNNNNN") self.assertEqual(contig.reads[5].qa.qual_clipping_start, 24) self.assertEqual(contig.reads[5].qa.qual_clipping_end, 706) self.assertEqual(contig.reads[5].qa.align_clipping_start, 24) self.assertEqual(contig.reads[5].qa.align_clipping_end, 706) self.assertEqual(contig.reads[5].ds.chromat_file, "") self.assertEqual(contig.reads[5].ds.phd_file, "") self.assertEqual(contig.reads[5].ds.time, "") self.assertEqual(contig.reads[5].ds.chem, "") self.assertEqual(contig.reads[5].ds.dye, "") self.assertEqual(contig.reads[5].ds.template, "") self.assertEqual(contig.reads[5].ds.direction, "") self.assertIsNone(contig.reads[5].rt) self.assertIsNone(contig.reads[5].wr) # Make sure there are no more contigs self.assertRaises(StopIteration, next, contigs) class AceTestThree(unittest.TestCase): """Test parsing example ACE input file for CONSED. The sample input file was downloaded from: http://bozeman.mbt.washington.edu/consed/distributions/README.16.0.txt """ def setUp(self): self.handle = open("Ace/consed_sample.ace") def tearDown(self): self.handle.close() def test_check_ACEParser(self): """Test to check that ACEParser can parse the whole file into one record.""" record = Ace.read(self.handle) self.assertEqual(record.ncontigs, 1) self.assertEqual(record.nreads, 8) self.assertEqual(len(record.wa), 1) self.assertEqual(record.wa[0].tag_type, "phrap_params") self.assertEqual(record.wa[0].program, "phrap") self.assertEqual(record.wa[0].date, "990621:161947") self.assertEqual( record.wa[0].info, [ "/usr/local/genome/bin/phrap standard.fasta.screen -new_ace -view", "phrap version 0.990319", ], ) self.assertEqual(len(record.contigs), 1) self.assertEqual(len(record.contigs[0].reads), 8) self.assertEqual(record.contigs[0].name, "Contig1") self.assertEqual(record.contigs[0].nbases, 1475) self.assertEqual(record.contigs[0].nreads, 8) self.assertEqual(record.contigs[0].nsegments, 156) self.assertEqual(record.contigs[0].uorc, "U") center = len(record.contigs[0].sequence) // 2 self.assertEqual(record.contigs[0].sequence[:10], "agccccgggc") self.assertEqual( record.contigs[0].sequence[center - 5 : center + 5], "CTTCCCCAGG" ) self.assertEqual(record.contigs[0].sequence[-10:], "gttgggtttg") center = len(record.contigs[0].quality) // 2 self.assertEqual(record.contigs[0].quality[:10], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) self.assertEqual( record.contigs[0].quality[center - 5 : center + 5], [90, 90, 90, 90, 90, 90, 90, 90, 89, 89], ) self.assertEqual( record.contigs[0].quality[-10:], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ) self.assertEqual(len(record.contigs[0].af), 8) self.assertEqual(len(record.contigs[0].bs), 156) self.assertEqual(record.contigs[0].af[4].name, "K26-291s") self.assertEqual(record.contigs[0].af[4].coru, "U") self.assertEqual(record.contigs[0].af[4].padded_start, 828) self.assertEqual(record.contigs[0].af[7].name, "K26-766c") self.assertEqual(record.contigs[0].af[7].coru, "C") self.assertEqual(record.contigs[0].af[7].padded_start, 408) self.assertEqual(record.contigs[0].bs[78].name, "K26-394c") self.assertEqual(record.contigs[0].bs[78].padded_start, 987) self.assertEqual(record.contigs[0].bs[78].padded_end, 987) self.assertEqual(record.contigs[0].bs[155].name, "K26-822c") self.assertEqual(record.contigs[0].bs[155].padded_start, 1303) self.assertEqual(record.contigs[0].bs[155].padded_end, 1475) self.assertEqual(len(record.contigs[0].ct), 3) self.assertEqual(record.contigs[0].ct[0].name, "Contig1") self.assertEqual(record.contigs[0].ct[0].tag_type, "repeat") self.assertEqual(record.contigs[0].ct[0].program, "consed") self.assertEqual(record.contigs[0].ct[0].padded_start, 976) self.assertEqual(record.contigs[0].ct[0].padded_end, 986) self.assertEqual(record.contigs[0].ct[0].date, "971218:180623") self.assertEqual(record.contigs[0].ct[0].info, []) self.assertEqual(record.contigs[0].ct[1].name, "Contig1") self.assertEqual(record.contigs[0].ct[1].tag_type, "comment") self.assertEqual(record.contigs[0].ct[1].program, "consed") self.assertEqual(record.contigs[0].ct[1].padded_start, 996) self.assertEqual(record.contigs[0].ct[1].padded_end, 1007) self.assertEqual(record.contigs[0].ct[1].date, "971218:180623") self.assertEqual( record.contigs[0].ct[1].info, ["This is line 1 of a comment", "There may be any number of lines"], ) self.assertEqual(record.contigs[0].ct[2].name, "Contig1") self.assertEqual(record.contigs[0].ct[2].tag_type, "oligo") self.assertEqual(record.contigs[0].ct[2].program, "consed") self.assertEqual(record.contigs[0].ct[2].padded_start, 963) self.assertEqual(record.contigs[0].ct[2].padded_end, 987) self.assertEqual(record.contigs[0].ct[2].date, "971218:180623") self.assertEqual( record.contigs[0].ct[2].info, ["standard.1 acataagacattctaaatttttact 50 U", "seq from clone"], ) self.assertEqual(len(record.contigs[0].wa), 1) self.assertEqual(record.contigs[0].wa[0].tag_type, "phrap_params") self.assertEqual(record.contigs[0].wa[0].program, "phrap") self.assertEqual(record.contigs[0].wa[0].date, "990621:161947") self.assertEqual( record.contigs[0].wa[0].info, [ "/usr/local/genome/bin/phrap standard.fasta.screen -new_ace -view", "phrap version 0.990319", ], ) self.assertEqual(len(record.contigs[0].reads), 8) self.assertEqual(record.contigs[0].reads[0].rd.name, "K26-217c") self.assertEqual(record.contigs[0].reads[0].rd.padded_bases, 563) self.assertEqual(record.contigs[0].reads[0].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[0].rd.read_tags, 0) center = len(record.contigs[0].reads[0].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[0].rd.sequence[:10], "tcccCgtgag") self.assertEqual( record.contigs[0].reads[0].rd.sequence[center - 5 : center + 5], "CTCCTGcctg", ) self.assertEqual(record.contigs[0].reads[0].rd.sequence[-10:], "ggcccccctc") self.assertEqual(record.contigs[0].reads[0].qa.qual_clipping_start, 19) self.assertEqual(record.contigs[0].reads[0].qa.qual_clipping_end, 349) self.assertEqual(record.contigs[0].reads[0].qa.align_clipping_start, 19) self.assertEqual(record.contigs[0].reads[0].qa.align_clipping_end, 424) self.assertEqual(record.contigs[0].reads[0].ds.chromat_file, "K26-217c") self.assertEqual(record.contigs[0].reads[0].ds.phd_file, "K26-217c.phd.1") self.assertEqual(record.contigs[0].reads[0].ds.time, "Thu Sep 12 15:42:38 1996") self.assertEqual(record.contigs[0].reads[0].ds.chem, "") self.assertEqual(record.contigs[0].reads[0].ds.dye, "") self.assertEqual(record.contigs[0].reads[0].ds.template, "") self.assertEqual(record.contigs[0].reads[0].ds.direction, "") self.assertIsNone(record.contigs[0].reads[0].rt) self.assertIsNone(record.contigs[0].reads[0].wr) self.assertEqual(record.contigs[0].reads[1].rd.name, "K26-526t") self.assertEqual(record.contigs[0].reads[1].rd.padded_bases, 687) self.assertEqual(record.contigs[0].reads[1].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[1].rd.read_tags, 0) center = len(record.contigs[0].reads[1].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[1].rd.sequence[:10], "ccgtcctgag") self.assertEqual( record.contigs[0].reads[1].rd.sequence[center - 5 : center + 5], "cacagcccT*", ) self.assertEqual(record.contigs[0].reads[1].rd.sequence[-10:], "Ttttgtttta") self.assertEqual(record.contigs[0].reads[1].qa.qual_clipping_start, 12) self.assertEqual(record.contigs[0].reads[1].qa.qual_clipping_end, 353) self.assertEqual(record.contigs[0].reads[1].qa.align_clipping_start, 9) self.assertEqual(record.contigs[0].reads[1].qa.align_clipping_end, 572) self.assertEqual(record.contigs[0].reads[1].ds.chromat_file, "K26-526t") self.assertEqual(record.contigs[0].reads[1].ds.phd_file, "K26-526t.phd.1") self.assertEqual(record.contigs[0].reads[1].ds.time, "Thu Sep 12 15:42:33 1996") self.assertEqual(record.contigs[0].reads[1].ds.chem, "") self.assertEqual(record.contigs[0].reads[1].ds.dye, "") self.assertEqual(record.contigs[0].reads[1].ds.template, "") self.assertEqual(record.contigs[0].reads[1].ds.direction, "") self.assertIsNone(record.contigs[0].reads[1].rt) self.assertIsNone(record.contigs[0].reads[1].wr) self.assertEqual(record.contigs[0].reads[2].rd.name, "K26-961c") self.assertEqual(record.contigs[0].reads[2].rd.padded_bases, 517) self.assertEqual(record.contigs[0].reads[2].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[2].rd.read_tags, 0) center = len(record.contigs[0].reads[2].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[2].rd.sequence[:10], "aatattaccg") self.assertEqual( record.contigs[0].reads[2].rd.sequence[center - 5 : center + 5], "CAGATGGGTT", ) self.assertEqual(record.contigs[0].reads[2].rd.sequence[-10:], "ctattcaggg") self.assertEqual(record.contigs[0].reads[2].qa.qual_clipping_start, 20) self.assertEqual(record.contigs[0].reads[2].qa.qual_clipping_end, 415) self.assertEqual(record.contigs[0].reads[2].qa.align_clipping_start, 26) self.assertEqual(record.contigs[0].reads[2].qa.align_clipping_end, 514) self.assertEqual(record.contigs[0].reads[2].ds.chromat_file, "K26-961c") self.assertEqual(record.contigs[0].reads[2].ds.phd_file, "K26-961c.phd.1") self.assertEqual(record.contigs[0].reads[2].ds.time, "Thu Sep 12 15:42:37 1996") self.assertEqual(record.contigs[0].reads[2].ds.chem, "") self.assertEqual(record.contigs[0].reads[2].ds.dye, "") self.assertEqual(record.contigs[0].reads[2].ds.template, "") self.assertEqual(record.contigs[0].reads[2].ds.direction, "") self.assertIsNone(record.contigs[0].reads[2].rt) self.assertIsNone(record.contigs[0].reads[2].wr) self.assertEqual(record.contigs[0].reads[3].rd.name, "K26-394c") self.assertEqual(record.contigs[0].reads[3].rd.padded_bases, 628) self.assertEqual(record.contigs[0].reads[3].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[3].rd.read_tags, 0) center = len(record.contigs[0].reads[3].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[3].rd.sequence[:10], "ctgcgtatcg") self.assertEqual( record.contigs[0].reads[3].rd.sequence[center - 5 : center + 5], "AGGATTGCTT", ) self.assertEqual(record.contigs[0].reads[3].rd.sequence[-10:], "aaccctgggt") self.assertEqual(record.contigs[0].reads[3].qa.qual_clipping_start, 18) self.assertEqual(record.contigs[0].reads[3].qa.qual_clipping_end, 368) self.assertEqual(record.contigs[0].reads[3].qa.align_clipping_start, 11) self.assertEqual(record.contigs[0].reads[3].qa.align_clipping_end, 502) self.assertEqual(record.contigs[0].reads[3].ds.chromat_file, "K26-394c") self.assertEqual(record.contigs[0].reads[3].ds.phd_file, "K26-394c.phd.1") self.assertEqual(record.contigs[0].reads[3].ds.time, "Thu Sep 12 15:42:32 1996") self.assertEqual(record.contigs[0].reads[3].ds.chem, "") self.assertEqual(record.contigs[0].reads[3].ds.dye, "") self.assertEqual(record.contigs[0].reads[3].ds.template, "") self.assertEqual(record.contigs[0].reads[3].ds.direction, "") self.assertIsNone(record.contigs[0].reads[3].rt) self.assertIsNone(record.contigs[0].reads[3].wr) self.assertEqual(record.contigs[0].reads[4].rd.name, "K26-291s") self.assertEqual(record.contigs[0].reads[4].rd.padded_bases, 556) self.assertEqual(record.contigs[0].reads[4].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[4].rd.read_tags, 0) center = len(record.contigs[0].reads[4].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[4].rd.sequence[:10], "gaggatcgct") self.assertEqual( record.contigs[0].reads[4].rd.sequence[center - 5 : center + 5], "GTgcgaggat", ) self.assertEqual(record.contigs[0].reads[4].rd.sequence[-10:], "caggcagatg") self.assertEqual(record.contigs[0].reads[4].qa.qual_clipping_start, 11) self.assertEqual(record.contigs[0].reads[4].qa.qual_clipping_end, 373) self.assertEqual(record.contigs[0].reads[4].qa.align_clipping_start, 11) self.assertEqual(record.contigs[0].reads[4].qa.align_clipping_end, 476) self.assertEqual(record.contigs[0].reads[4].ds.chromat_file, "K26-291s") self.assertEqual(record.contigs[0].reads[4].ds.phd_file, "K26-291s.phd.1") self.assertEqual(record.contigs[0].reads[4].ds.time, "Thu Sep 12 15:42:31 1996") self.assertEqual(record.contigs[0].reads[4].ds.chem, "") self.assertEqual(record.contigs[0].reads[4].ds.dye, "") self.assertEqual(record.contigs[0].reads[4].ds.template, "") self.assertEqual(record.contigs[0].reads[4].ds.direction, "") self.assertIsNone(record.contigs[0].reads[4].rt) self.assertIsNone(record.contigs[0].reads[4].wr) self.assertEqual(record.contigs[0].reads[5].rd.name, "K26-822c") self.assertEqual(record.contigs[0].reads[5].rd.padded_bases, 593) self.assertEqual(record.contigs[0].reads[5].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[5].rd.read_tags, 0) center = len(record.contigs[0].reads[5].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[5].rd.sequence[:10], "ggggatccg*") self.assertEqual( record.contigs[0].reads[5].rd.sequence[center - 5 : center + 5], "GCaAgacCCt", ) self.assertEqual(record.contigs[0].reads[5].rd.sequence[-10:], "gttgggtttg") self.assertEqual(record.contigs[0].reads[5].qa.qual_clipping_start, 25) self.assertEqual(record.contigs[0].reads[5].qa.qual_clipping_end, 333) self.assertEqual(record.contigs[0].reads[5].qa.align_clipping_start, 16) self.assertEqual(record.contigs[0].reads[5].qa.align_clipping_end, 593) self.assertEqual(record.contigs[0].reads[5].ds.chromat_file, "K26-822c") self.assertEqual(record.contigs[0].reads[5].ds.phd_file, "K26-822c.phd.1") self.assertEqual(record.contigs[0].reads[5].ds.time, "Thu Sep 12 15:42:36 1996") self.assertEqual(record.contigs[0].reads[5].ds.chem, "") self.assertEqual(record.contigs[0].reads[5].ds.dye, "") self.assertEqual(record.contigs[0].reads[5].ds.template, "") self.assertEqual(record.contigs[0].reads[5].ds.direction, "") self.assertIsNone(record.contigs[0].reads[5].rt) self.assertIsNone(record.contigs[0].reads[5].wr) self.assertEqual(record.contigs[0].reads[6].rd.name, "K26-572c") self.assertEqual(record.contigs[0].reads[6].rd.padded_bases, 594) self.assertEqual(record.contigs[0].reads[6].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[6].rd.read_tags, 0) center = len(record.contigs[0].reads[6].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[6].rd.sequence[:10], "agccccgggc") self.assertEqual( record.contigs[0].reads[6].rd.sequence[center - 5 : center + 5], "ggatcACATA", ) self.assertEqual(record.contigs[0].reads[6].rd.sequence[-10:], "aatagtaaca") self.assertEqual(record.contigs[0].reads[6].qa.qual_clipping_start, 249) self.assertEqual(record.contigs[0].reads[6].qa.qual_clipping_end, 584) self.assertEqual(record.contigs[0].reads[6].qa.align_clipping_start, 1) self.assertEqual(record.contigs[0].reads[6].qa.align_clipping_end, 586) self.assertEqual(record.contigs[0].reads[6].ds.chromat_file, "K26-572c") self.assertEqual(record.contigs[0].reads[6].ds.phd_file, "K26-572c.phd.1") self.assertEqual(record.contigs[0].reads[6].ds.time, "Thu Sep 12 15:42:34 1996") self.assertEqual(record.contigs[0].reads[6].ds.chem, "") self.assertEqual(record.contigs[0].reads[6].ds.dye, "") self.assertEqual(record.contigs[0].reads[6].ds.template, "") self.assertEqual(record.contigs[0].reads[6].ds.direction, "") self.assertIsNone(record.contigs[0].reads[6].rt) self.assertIsNone(record.contigs[0].reads[6].wr) self.assertEqual(record.contigs[0].reads[7].rd.name, "K26-766c") self.assertEqual(record.contigs[0].reads[7].rd.padded_bases, 603) self.assertEqual(record.contigs[0].reads[7].rd.info_items, 0) self.assertEqual(record.contigs[0].reads[7].rd.read_tags, 0) center = len(record.contigs[0].reads[7].rd.sequence) // 2 self.assertEqual(record.contigs[0].reads[7].rd.sequence[:10], "gaataattgg") self.assertEqual( record.contigs[0].reads[7].rd.sequence[center - 5 : center + 5], "TggCCCATCT", ) self.assertEqual(record.contigs[0].reads[7].rd.sequence[-10:], "gaaccacacg") self.assertEqual(record.contigs[0].reads[7].qa.qual_clipping_start, 240) self.assertEqual(record.contigs[0].reads[7].qa.qual_clipping_end, 584) self.assertEqual(record.contigs[0].reads[7].qa.align_clipping_start, 126) self.assertEqual(record.contigs[0].reads[7].qa.align_clipping_end, 583) self.assertEqual(record.contigs[0].reads[7].ds.chromat_file, "K26-766c") self.assertEqual(record.contigs[0].reads[7].ds.phd_file, "K26-766c.phd.1") self.assertEqual(record.contigs[0].reads[7].ds.time, "Thu Sep 12 15:42:35 1996") self.assertEqual(record.contigs[0].reads[7].ds.chem, "") self.assertEqual(record.contigs[0].reads[7].ds.dye, "") self.assertEqual(record.contigs[0].reads[7].ds.template, "") self.assertEqual(record.contigs[0].reads[7].ds.direction, "") self.assertIsNone(record.contigs[0].reads[7].rt) self.assertIsNone(record.contigs[0].reads[7].wr) def test_check_record_parser(self): """Test to check that record parser parses each contig into a record.""" contigs = Ace.parse(self.handle) # First (and only) contig contig = next(contigs) self.assertEqual(len(contig.reads), 8) self.assertEqual(contig.name, "Contig1") self.assertEqual(contig.nbases, 1475) self.assertEqual(contig.nreads, 8) self.assertEqual(contig.nsegments, 156) self.assertEqual(contig.uorc, "U") center = len(contig.sequence) // 2 self.assertEqual(contig.sequence[:10], "agccccgggc") self.assertEqual(contig.sequence[center - 5 : center + 5], "CTTCCCCAGG") self.assertEqual(contig.sequence[-10:], "gttgggtttg") center = len(contig.quality) // 2 self.assertEqual(contig.quality[:10], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) self.assertEqual( contig.quality[center - 5 : center + 5], [90, 90, 90, 90, 90, 90, 90, 90, 89, 89], ) self.assertEqual(contig.quality[-10:], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) self.assertEqual(len(contig.af), 8) self.assertEqual(len(contig.bs), 156) self.assertEqual(contig.af[4].name, "K26-291s") self.assertEqual(contig.af[4].coru, "U") self.assertEqual(contig.af[4].padded_start, 828) self.assertEqual(contig.af[7].name, "K26-766c") self.assertEqual(contig.af[7].coru, "C") self.assertEqual(contig.af[7].padded_start, 408) self.assertEqual(contig.bs[78].name, "K26-394c") self.assertEqual(contig.bs[78].padded_start, 987) self.assertEqual(contig.bs[78].padded_end, 987) self.assertEqual(contig.bs[155].name, "K26-822c") self.assertEqual(contig.bs[155].padded_start, 1303) self.assertEqual(contig.bs[155].padded_end, 1475) self.assertEqual(len(contig.ct), 3) self.assertEqual(contig.ct[0].name, "Contig1") self.assertEqual(contig.ct[0].tag_type, "repeat") self.assertEqual(contig.ct[0].program, "consed") self.assertEqual(contig.ct[0].padded_start, 976) self.assertEqual(contig.ct[0].padded_end, 986) self.assertEqual(contig.ct[0].date, "971218:180623") self.assertEqual(contig.ct[0].info, []) self.assertEqual(contig.ct[1].name, "Contig1") self.assertEqual(contig.ct[1].tag_type, "comment") self.assertEqual(contig.ct[1].program, "consed") self.assertEqual(contig.ct[1].padded_start, 996) self.assertEqual(contig.ct[1].padded_end, 1007) self.assertEqual(contig.ct[1].date, "971218:180623") self.assertEqual( contig.ct[1].info, ["This is line 1 of a comment", "There may be any number of lines"], ) self.assertEqual(contig.ct[2].name, "Contig1") self.assertEqual(contig.ct[2].tag_type, "oligo") self.assertEqual(contig.ct[2].program, "consed") self.assertEqual(contig.ct[2].padded_start, 963) self.assertEqual(contig.ct[2].padded_end, 987) self.assertEqual(contig.ct[2].date, "971218:180623") self.assertEqual( contig.ct[2].info, ["standard.1 acataagacattctaaatttttact 50 U", "seq from clone"], ) self.assertEqual(len(contig.wa), 1) self.assertEqual(contig.wa[0].tag_type, "phrap_params") self.assertEqual(contig.wa[0].program, "phrap") self.assertEqual(contig.wa[0].date, "990621:161947") self.assertEqual( contig.wa[0].info, [ "/usr/local/genome/bin/phrap standard.fasta.screen -new_ace -view", "phrap version 0.990319", ], ) self.assertEqual(len(contig.reads), 8) self.assertEqual(contig.reads[0].rd.name, "K26-217c") self.assertEqual(contig.reads[0].rd.padded_bases, 563) self.assertEqual(contig.reads[0].rd.info_items, 0) self.assertEqual(contig.reads[0].rd.read_tags, 0) center = len(contig.reads[0].rd.sequence) // 2 self.assertEqual(contig.reads[0].rd.sequence[:10], "tcccCgtgag") self.assertEqual( contig.reads[0].rd.sequence[center - 5 : center + 5], "CTCCTGcctg" ) self.assertEqual(contig.reads[0].rd.sequence[-10:], "ggcccccctc") self.assertEqual(contig.reads[0].qa.qual_clipping_start, 19) self.assertEqual(contig.reads[0].qa.qual_clipping_end, 349) self.assertEqual(contig.reads[0].qa.align_clipping_start, 19) self.assertEqual(contig.reads[0].qa.align_clipping_end, 424) self.assertEqual(contig.reads[0].ds.chromat_file, "K26-217c") self.assertEqual(contig.reads[0].ds.phd_file, "K26-217c.phd.1") self.assertEqual(contig.reads[0].ds.time, "Thu Sep 12 15:42:38 1996") self.assertEqual(contig.reads[0].ds.chem, "") self.assertEqual(contig.reads[0].ds.dye, "") self.assertEqual(contig.reads[0].ds.template, "") self.assertEqual(contig.reads[0].ds.direction, "") self.assertIsNone(contig.reads[0].rt) self.assertIsNone(contig.reads[0].wr) self.assertEqual(contig.reads[1].rd.name, "K26-526t") self.assertEqual(contig.reads[1].rd.padded_bases, 687) self.assertEqual(contig.reads[1].rd.info_items, 0) self.assertEqual(contig.reads[1].rd.read_tags, 0) center = len(contig.reads[1].rd.sequence) // 2 self.assertEqual(contig.reads[1].rd.sequence[:10], "ccgtcctgag") self.assertEqual( contig.reads[1].rd.sequence[center - 5 : center + 5], "cacagcccT*" ) self.assertEqual(contig.reads[1].rd.sequence[-10:], "Ttttgtttta") self.assertEqual(contig.reads[1].qa.qual_clipping_start, 12) self.assertEqual(contig.reads[1].qa.qual_clipping_end, 353) self.assertEqual(contig.reads[1].qa.align_clipping_start, 9) self.assertEqual(contig.reads[1].qa.align_clipping_end, 572) self.assertEqual(contig.reads[1].ds.chromat_file, "K26-526t") self.assertEqual(contig.reads[1].ds.phd_file, "K26-526t.phd.1") self.assertEqual(contig.reads[1].ds.time, "Thu Sep 12 15:42:33 1996") self.assertEqual(contig.reads[1].ds.chem, "") self.assertEqual(contig.reads[1].ds.dye, "") self.assertEqual(contig.reads[1].ds.template, "") self.assertEqual(contig.reads[1].ds.direction, "") self.assertIsNone(contig.reads[1].rt) self.assertIsNone(contig.reads[1].wr) self.assertEqual(contig.reads[2].rd.name, "K26-961c") self.assertEqual(contig.reads[2].rd.padded_bases, 517) self.assertEqual(contig.reads[2].rd.info_items, 0) self.assertEqual(contig.reads[2].rd.read_tags, 0) center = len(contig.reads[2].rd.sequence) // 2 self.assertEqual(contig.reads[2].rd.sequence[:10], "aatattaccg") self.assertEqual( contig.reads[2].rd.sequence[center - 5 : center + 5], "CAGATGGGTT" ) self.assertEqual(contig.reads[2].rd.sequence[-10:], "ctattcaggg") self.assertEqual(contig.reads[2].qa.qual_clipping_start, 20) self.assertEqual(contig.reads[2].qa.qual_clipping_end, 415) self.assertEqual(contig.reads[2].qa.align_clipping_start, 26) self.assertEqual(contig.reads[2].qa.align_clipping_end, 514) self.assertEqual(contig.reads[2].ds.chromat_file, "K26-961c") self.assertEqual(contig.reads[2].ds.phd_file, "K26-961c.phd.1") self.assertEqual(contig.reads[2].ds.time, "Thu Sep 12 15:42:37 1996") self.assertEqual(contig.reads[2].ds.chem, "") self.assertEqual(contig.reads[2].ds.dye, "") self.assertEqual(contig.reads[2].ds.template, "") self.assertEqual(contig.reads[2].ds.direction, "") self.assertIsNone(contig.reads[2].rt) self.assertIsNone(contig.reads[2].wr) self.assertEqual(contig.reads[3].rd.name, "K26-394c") self.assertEqual(contig.reads[3].rd.padded_bases, 628) self.assertEqual(contig.reads[3].rd.info_items, 0) self.assertEqual(contig.reads[3].rd.read_tags, 0) center = len(contig.reads[3].rd.sequence) // 2 self.assertEqual(contig.reads[3].rd.sequence[:10], "ctgcgtatcg") self.assertEqual( contig.reads[3].rd.sequence[center - 5 : center + 5], "AGGATTGCTT" ) self.assertEqual(contig.reads[3].rd.sequence[-10:], "aaccctgggt") self.assertEqual(contig.reads[3].qa.qual_clipping_start, 18) self.assertEqual(contig.reads[3].qa.qual_clipping_end, 368) self.assertEqual(contig.reads[3].qa.align_clipping_start, 11) self.assertEqual(contig.reads[3].qa.align_clipping_end, 502) self.assertEqual(contig.reads[3].ds.chromat_file, "K26-394c") self.assertEqual(contig.reads[3].ds.phd_file, "K26-394c.phd.1") self.assertEqual(contig.reads[3].ds.time, "Thu Sep 12 15:42:32 1996") self.assertEqual(contig.reads[3].ds.chem, "") self.assertEqual(contig.reads[3].ds.dye, "") self.assertEqual(contig.reads[3].ds.template, "") self.assertEqual(contig.reads[3].ds.direction, "") self.assertIsNone(contig.reads[3].rt) self.assertIsNone(contig.reads[3].wr) self.assertEqual(contig.reads[4].rd.name, "K26-291s") self.assertEqual(contig.reads[4].rd.padded_bases, 556) self.assertEqual(contig.reads[4].rd.info_items, 0) self.assertEqual(contig.reads[4].rd.read_tags, 0) center = len(contig.reads[4].rd.sequence) // 2 self.assertEqual(contig.reads[4].rd.sequence[:10], "gaggatcgct") self.assertEqual( contig.reads[4].rd.sequence[center - 5 : center + 5], "GTgcgaggat" ) self.assertEqual(contig.reads[4].rd.sequence[-10:], "caggcagatg") self.assertEqual(contig.reads[4].qa.qual_clipping_start, 11) self.assertEqual(contig.reads[4].qa.qual_clipping_end, 373) self.assertEqual(contig.reads[4].qa.align_clipping_start, 11) self.assertEqual(contig.reads[4].qa.align_clipping_end, 476) self.assertEqual(contig.reads[4].ds.chromat_file, "K26-291s") self.assertEqual(contig.reads[4].ds.phd_file, "K26-291s.phd.1") self.assertEqual(contig.reads[4].ds.time, "Thu Sep 12 15:42:31 1996") self.assertEqual(contig.reads[4].ds.chem, "") self.assertEqual(contig.reads[4].ds.dye, "") self.assertEqual(contig.reads[4].ds.template, "") self.assertEqual(contig.reads[4].ds.direction, "") self.assertIsNone(contig.reads[4].rt) self.assertIsNone(contig.reads[4].wr) self.assertEqual(contig.reads[5].rd.name, "K26-822c") self.assertEqual(contig.reads[5].rd.padded_bases, 593) self.assertEqual(contig.reads[5].rd.info_items, 0) self.assertEqual(contig.reads[5].rd.read_tags, 0) center = len(contig.reads[5].rd.sequence) // 2 self.assertEqual(contig.reads[5].rd.sequence[:10], "ggggatccg*") self.assertEqual( contig.reads[5].rd.sequence[center - 5 : center + 5], "GCaAgacCCt" ) self.assertEqual(contig.reads[5].rd.sequence[-10:], "gttgggtttg") self.assertEqual(contig.reads[5].qa.qual_clipping_start, 25) self.assertEqual(contig.reads[5].qa.qual_clipping_end, 333) self.assertEqual(contig.reads[5].qa.align_clipping_start, 16) self.assertEqual(contig.reads[5].qa.align_clipping_end, 593) self.assertEqual(contig.reads[5].ds.chromat_file, "K26-822c") self.assertEqual(contig.reads[5].ds.phd_file, "K26-822c.phd.1") self.assertEqual(contig.reads[5].ds.time, "Thu Sep 12 15:42:36 1996") self.assertEqual(contig.reads[5].ds.chem, "") self.assertEqual(contig.reads[5].ds.dye, "") self.assertEqual(contig.reads[5].ds.template, "") self.assertEqual(contig.reads[5].ds.direction, "") self.assertIsNone(contig.reads[5].rt) self.assertIsNone(contig.reads[5].wr) self.assertEqual(contig.reads[6].rd.name, "K26-572c") self.assertEqual(contig.reads[6].rd.padded_bases, 594) self.assertEqual(contig.reads[6].rd.info_items, 0) self.assertEqual(contig.reads[6].rd.read_tags, 0) center = len(contig.reads[6].rd.sequence) // 2 self.assertEqual(contig.reads[6].rd.sequence[:10], "agccccgggc") self.assertEqual( contig.reads[6].rd.sequence[center - 5 : center + 5], "ggatcACATA" ) self.assertEqual(contig.reads[6].rd.sequence[-10:], "aatagtaaca") self.assertEqual(contig.reads[6].qa.qual_clipping_start, 249) self.assertEqual(contig.reads[6].qa.qual_clipping_end, 584) self.assertEqual(contig.reads[6].qa.align_clipping_start, 1) self.assertEqual(contig.reads[6].qa.align_clipping_end, 586) self.assertEqual(contig.reads[6].ds.chromat_file, "K26-572c") self.assertEqual(contig.reads[6].ds.phd_file, "K26-572c.phd.1") self.assertEqual(contig.reads[6].ds.time, "Thu Sep 12 15:42:34 1996") self.assertEqual(contig.reads[6].ds.chem, "") self.assertEqual(contig.reads[6].ds.dye, "") self.assertEqual(contig.reads[6].ds.template, "") self.assertEqual(contig.reads[6].ds.direction, "") self.assertIsNone(contig.reads[6].rt) self.assertIsNone(contig.reads[6].wr) self.assertEqual(contig.reads[7].rd.name, "K26-766c") self.assertEqual(contig.reads[7].rd.padded_bases, 603) self.assertEqual(contig.reads[7].rd.info_items, 0) self.assertEqual(contig.reads[7].rd.read_tags, 0) center = len(contig.reads[7].rd.sequence) // 2 self.assertEqual(contig.reads[7].rd.sequence[:10], "gaataattgg") self.assertEqual( contig.reads[7].rd.sequence[center - 5 : center + 5], "TggCCCATCT" ) self.assertEqual(contig.reads[7].rd.sequence[-10:], "gaaccacacg") self.assertEqual(contig.reads[7].qa.qual_clipping_start, 240) self.assertEqual(contig.reads[7].qa.qual_clipping_end, 584) self.assertEqual(contig.reads[7].qa.align_clipping_start, 126) self.assertEqual(contig.reads[7].qa.align_clipping_end, 583) self.assertEqual(contig.reads[7].ds.chromat_file, "K26-766c") self.assertEqual(contig.reads[7].ds.phd_file, "K26-766c.phd.1") self.assertEqual(contig.reads[7].ds.time, "Thu Sep 12 15:42:35 1996") self.assertEqual(contig.reads[7].ds.chem, "") self.assertEqual(contig.reads[7].ds.dye, "") self.assertEqual(contig.reads[7].ds.template, "") self.assertEqual(contig.reads[7].ds.direction, "") self.assertIsNone(contig.reads[7].rt) self.assertIsNone(contig.reads[7].wr) # Make sure there are no more contigs self.assertRaises(StopIteration, next, contigs) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)