# Copyright 2011 by Peter Cock. 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. """Unit tests for the Bio.AlignIO.FastaIO module.""" import unittest from Bio.AlignIO import FastaIO class FastaIOTests(unittest.TestCase): """Test FastaIO module.""" def test_output001(self): """Check output001.m10 file.""" fasta_file = 'Fasta/output001.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 4) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 108) self.assertEqual(alignments[0][0].seq, "SGSNT-RRRAISRPVRLTAEED---QE" "IRKRAAECGKTVSGFLRAAALGKKVNS" "LTDDRVLKEVM-----RLGALQKKLFI" "DGKRVGDREYAEVLIAITEYHRALLSR") self.assertEqual(alignments[0][0].id, "gi|10955263|ref|NP_052604.1|") self.assertEqual(alignments[0][0].annotations["original_length"], 107) self.assertEqual(alignments[0][1].seq, "AGSGAPRRRGSGLASRISEQSEALLQE" "AAKHAAEFGRS------EVDTEHLLLA" "LADSDVVKTILGQFKIKVDDLKRQIES" "EAKR-GDKPF-EGEIGVSPRVKDALSR") self.assertEqual(alignments[0][1].id, "gi|152973457|ref|YP_001338508.1|") self.assertEqual(alignments[0][1].annotations["original_length"], 931) self.assertEqual(len(alignments[1]), 2) self.assertEqual(alignments[1].get_alignment_length(), 64) self.assertEqual(alignments[1][0].seq, "AAECGKTVSGFLRAAALGKKVNSLTDD" "RVLKEV-MRLGALQKKLFIDGKRVGDR" "EYAEVLIAIT") self.assertEqual(alignments[1][0].id, "gi|10955263|ref|NP_052604.1|") self.assertEqual(alignments[1][0].annotations["original_length"], 107) self.assertEqual(alignments[1][1].seq, "ASRQGCTVGG--KMDSVQDKASDKDKE" "RVMKNINIMWNALSKNRLFDG----NK" "ELKEFIMTLT") self.assertEqual(alignments[1][1].id, "gi|152973588|ref|YP_001338639.1|") self.assertEqual(alignments[1][1].annotations["original_length"], 459) self.assertEqual(len(alignments[2]), 2) self.assertEqual(alignments[2].get_alignment_length(), 38) self.assertEqual(alignments[2][0].seq, "MKKDKKYQIEAIKNKDKTLFIVYATDI" "YSPSEFFSKIE") self.assertEqual(alignments[2][0].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[2][0].annotations["original_length"], 126) self.assertEqual(alignments[2][1].seq, "IKKDLGVSFLKLKNREKTLIVDALKKK" "YPVAELLSVLQ") self.assertEqual(alignments[2][1].id, "gi|152973462|ref|YP_001338513.1|") self.assertEqual(alignments[2][1].annotations["original_length"], 101) self.assertEqual(len(alignments[3]), 2) self.assertEqual(alignments[3].get_alignment_length(), 43) self.assertEqual(alignments[3][0].seq, "SELHSKLPKSIDKIHEDIKKQLSC-SL" "IMKKIDVEMEDYSTYC") self.assertEqual(alignments[3][0].id, "gi|10955265|ref|NP_052606.1|") self.assertEqual(alignments[3][0].annotations["original_length"], 346) self.assertEqual(alignments[3][1].seq, "SRINSDVARRIPGIHRDPKDRLSSLKQ" "VEEALDMLISSHGEYC") self.assertEqual(alignments[3][1].id, "gi|152973545|ref|YP_001338596.1|") self.assertEqual(alignments[3][1].annotations["original_length"], 242) def test_output002(self): """Check output002.m10 file.""" fasta_file = 'Fasta/output002.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 6) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 88) self.assertEqual(alignments[0][0].seq, "SGSNTRRRAISRPVR--LTAEED" "QEIRKRAAECG-KTVSGFLRAAA" "LGKKVNSLTDDRVLKEVMRLGAL" "QKKLFIDGKRVGDREYAEV") self.assertEqual(alignments[0][0].id, "gi|10955263|ref|NP_052604.1|") self.assertEqual(alignments[0][0].annotations["original_length"], 107) self.assertEqual(alignments[0][1].seq, "SQRSTRRKPENQPTRVILFNKPY" "DVLPQFTDEAGRKTLKEFIPVQG" "VYAAGRLDRDSEGLLVLTNNGAL" "QARLTQPGKRTGKIYYVQV") self.assertEqual(alignments[0][1].id, "gi|162139799|ref|NP_309634.2|") self.assertEqual(alignments[0][1].annotations["original_length"], 207) self.assertEqual(len(alignments[1]), 2) self.assertEqual(alignments[1].get_alignment_length(), 53) self.assertEqual(alignments[1][0].seq, "EIRKRAAECGKTVSGFLRAAA-L" "GKKV----NSLTDDRVLKEVMRL" "GALQKKL") self.assertEqual(alignments[1][0].id, "gi|10955263|ref|NP_052604.1|") self.assertEqual(alignments[1][0].annotations["original_length"], 107) self.assertEqual(alignments[1][1].seq, "EIKPRGTSKGEAIAAFMQEAPFI" "GRTPVFLGDDLTDESGFAVVNRL" "GGMSVKI") self.assertEqual(alignments[1][1].id, "gi|15831859|ref|NP_310632.1|") self.assertEqual(alignments[1][1].annotations["original_length"], 266) self.assertEqual(len(alignments[2]), 2) self.assertEqual(alignments[2].get_alignment_length(), 92) self.assertEqual(alignments[2][0].seq, "SEFFSKIESDLKKKKSKGDVFFD" "LIIPNG-----GKKDRYVYTSFN" "GEKFSSYTLNKVTKTDEYNDLSE" "LSASFFKKNFDKINVNLLSKATS") self.assertEqual(alignments[2][0].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[2][0].annotations["original_length"], 126) self.assertEqual(alignments[2][1].seq, "TELNSELAKAMKVDAQRG-AFVS" "QVLPNSSAAKAGIKAGDVITSL" "NGKPISSFAALRA-QVGTMPVG" "SKLTLGLLRDG-KQVNVNLELQ" "QSS") self.assertEqual(alignments[2][1].id, "gi|15829419|ref|NP_308192.1|") self.assertEqual(alignments[2][1].annotations["original_length"], 474) self.assertEqual(len(alignments[3]), 2) self.assertEqual(alignments[3].get_alignment_length(), 73) self.assertEqual(alignments[3][0].seq, "FFDLIIPNGGKKDRYVYTSFNGE" "KFSSYTLNKVTKTDEYNDLSELS" "ASFFKKNFDKINVNLLSKATSFA" "LKKG") self.assertEqual(alignments[3][0].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[3][0].annotations["original_length"], 126) self.assertEqual(alignments[3][1].seq, "LFDLFLKNDAMHDPMVNESYC-E" "TFGWVSKENLARMKE---LTYKA" "NDVLKKLFDDAGLILVDFKLEFG" "LYKG") self.assertEqual(alignments[3][1].id, "gi|15832592|ref|NP_311365.1|") self.assertEqual(alignments[3][1].annotations["original_length"], 237) self.assertEqual(len(alignments[4]), 2) self.assertEqual(alignments[4].get_alignment_length(), 63) self.assertEqual(alignments[4][0].seq, "VDIKK-ETIESELHSKLPKSIDK" "IHEDIKKQLSCSLI--MKKID-V" "EMEDYSTYCFSALRAIE") self.assertEqual(alignments[4][0].id, "gi|10955265|ref|NP_052606.1|") self.assertEqual(alignments[4][0].annotations["original_length"], 346) self.assertEqual(alignments[4][1].seq, "IDPKKIEQIARQVHESMPKGIRE" "FGEDVEKKIRQTLQAQLTRLDLV" "SREEFDVQTQVLLRTRE") self.assertEqual(alignments[4][1].id, "gi|38704138|ref|NP_311957.2|") self.assertEqual(alignments[4][1].annotations["original_length"], 111) self.assertEqual(len(alignments[5]), 2) self.assertEqual(alignments[5].get_alignment_length(), 157) self.assertEqual(alignments[5][0].seq, "QYIMTTSNGDRVRAKIYKRGSIQ" "FQGKYLQIASLINDFMCSILNMK" "EIVEQKNKEFNVDI---KKETI-" "ESELHSKLPKSIDKIHEDIKKQL" "SCSLIMKKIDV-EMEDYSTYCFS" "ALRA-IEGFIYQILNDVCNPSSS" "KNLGEYFTENKPKYIIREI") self.assertEqual(alignments[5][0].id, "gi|10955265|ref|NP_052606.1|") self.assertEqual(alignments[5][0].annotations["original_length"], 346) self.assertEqual(alignments[5][1].seq, "EFIRLLSDHDQFEKDQISELTVA" "ANALKLEVAK--NNY-----NMK" "YSFDTQTERRMIELIREQKDLIP" "EKYLHQSGIKKL-KLHED---EF" "SSLLVDAERQVLEGSSFVLCCGE" "KINSTISELLSKKITDLTHPTES" "FTLSEYFSYDVYEEIFKKV") self.assertEqual(alignments[5][1].id, "gi|15833861|ref|NP_312634.1|") self.assertEqual(alignments[5][1].annotations["original_length"], 330) def test_output003(self): """Check output003.m10 file.""" fasta_file = 'Fasta/output003.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 3) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 55) self.assertEqual(alignments[0][0].seq, "ISISNNKDQYEELQKEQGERDLK" "TVDQLVRIAAAGGGLRLSASTKT" "VDQLVRIAA") self.assertEqual(alignments[0][0].id, "gi|152973837|ref|YP_001338874.1|") self.assertEqual(alignments[0][0].annotations["original_length"], 183) self.assertEqual(alignments[0][1].seq, "VRLTAEEDQ--EIRKRAAECG-K" "TVSGFLRAAALGKKVNSLTDDR" "VLKEVMRLGA") self.assertEqual(alignments[0][1].id, "gi|10955263|ref|NP_052604.1|") self.assertEqual(alignments[0][1].annotations["original_length"], 107) self.assertEqual(len(alignments[1]), 2) self.assertEqual(alignments[1].get_alignment_length(), 22) self.assertEqual(alignments[1][0].seq, "DDAEHLFRTLSSR-LDALQDGN") self.assertEqual(alignments[1][0].id, "gi|152973840|ref|YP_001338877.1|") self.assertEqual(alignments[1][0].annotations["original_length"], 63) self.assertEqual(alignments[1][1].seq, "DDRANLFEFLSEEGITITEDNN") self.assertEqual(alignments[1][1].id, "gi|10955265|ref|NP_052606.1|") self.assertEqual(alignments[1][1].annotations["original_length"], 346) self.assertEqual(len(alignments[2]), 2) self.assertEqual(alignments[2].get_alignment_length(), 63) self.assertEqual(alignments[2][0].seq, "VFGSFEQPKGEHLSGQVSEQ--R" "DTAFADQNEQVIRHLKQEIEHLN" "TLLLSKDSHIDSLKQAM") self.assertEqual(alignments[2][0].id, "gi|152973841|ref|YP_001338878.1|") self.assertEqual(alignments[2][0].annotations["original_length"], 133) self.assertEqual(alignments[2][1].seq, "VYTSFN---GEKFSSYTLNKVTK" "TDEYNDLSELSASFFKKNFDKIN" "VNLLSKATSF-ALKKGI") self.assertEqual(alignments[2][1].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[2][1].annotations["original_length"], 126) def test_output004(self): """Check output004.m10 file.""" fasta_file = 'Fasta/output004.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 1) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 102) self.assertEqual(alignments[0][0].seq, "AAAAAAGATAAAAAATATCAAAT" "AGAAGCAATAAAAAATAAAGATA" "AAACTTTATTTATTGTCTATGCT" "ACTGATATTTATAGCCCGAGCGA" "ATTTTTCTCA") self.assertEqual(alignments[0][0].id, "ref|NC_002127.1|:c1351-971") self.assertEqual(alignments[0][0].annotations["original_length"], 381) self.assertEqual(alignments[0][1].seq, "AGAGAAAATAAAACAAGTAATAA" "AATATTAATGGAAAAAATAAATT" "CTTGTTTATTTAGACCTGATTCT" "AATCACTTTTCTTGCCCGGAGTC" "ATTTTTGACA") self.assertEqual(alignments[0][1].id, "ref|NC_002695.1|:1970775-1971404") self.assertEqual(alignments[0][1].annotations["original_length"], 630) def test_output005(self): """Check output005.m10 file.""" fasta_file = 'Fasta/output005.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 1) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 110) self.assertEqual(alignments[0][0].seq, "IKNKDKTLFIVYAT-DIYSPSEF" "FSKIESDLKKKKSKGDV--FFDL" "IIPNGGKKD--RYVYTSFNGEKF" "SSYTLNKVTKTDEYNDL--SELS" "ASFFKKNFDKINVNLLSK") self.assertEqual(alignments[0][0].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[0][0].annotations["original_length"], 126) self.assertEqual(alignments[0][1].seq, "IKDELPVAFCSWASLDLECEVKY" "INDVTSLYAKDWMSGERKWFIDW" "IAPFGHNMELYKYMRKKYPYELF" "RAIRLDESSKTGKIAEFHGGGID" "KKLASKIFRQYHHELMSE") self.assertEqual(alignments[0][1].id, "gi|10955282|ref|NP_052623.1|") self.assertEqual(alignments[0][1].annotations["original_length"], 163) def test_output006(self): """Check output006.m10 file.""" fasta_file = 'Fasta/output006.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 1) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 131) self.assertEqual(alignments[0][0].seq, "GCAACGCTTCAAGAACTGGAATT" "AGGAACCGTGACAACGATTAATG" "AGGAGATTTATGAAGAGGGTTCT" "TCGATTTTAGGCCAATCGGAAGG" "AATTATGTAGCAAGTCCATCAGA" "AAATGGAAGAAGTCAT") self.assertEqual(alignments[0][0].id, "query") self.assertEqual(alignments[0][0].annotations["original_length"], 131) self.assertEqual(alignments[0][1].seq, "GCAACGCTTCAAGAACTGGAATT" "AGGAACCGTGACAACGATTAATG" "AGGAGATTTATGAAGAGGGTTCT" "TCGATTTTAGGCCAATCGGAAGG" "AATTATGTAGCAAGTCCATCAGA" "AAATGGAAGTAGTCAT") self.assertEqual(alignments[0][1].id, "gi|116660610|gb|EG558221.1|EG558221") self.assertEqual(alignments[0][1].annotations["original_length"], 573) def test_output007(self): """Check output007.m10 file.""" fasta_file = 'Fasta/output007.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 9) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 108) self.assertEqual(alignments[0][0].seq, "SGSNT-RRRAISRPVRLTAEED-" "--QEIRKRAAECGKTVSGFLRAA" "ALGKKVNSLTDDRVLKEVM----" "-RLGALQKKLFIDGKRVGDREYA" "EVLIAITEYHRALLSR") self.assertEqual(alignments[0][0].id, "gi|10955263|ref|NP_052604.1|") self.assertEqual(alignments[0][0].annotations["original_length"], 107) self.assertEqual(alignments[0][1].seq, "AGSGAPRRRGSGLASRISEQSEA" "LLQEAAKHAAEFGRS------EV" "DTEHLLLALADSDVVKTILGQFK" "IKVDDLKRQIESEAKR-GDKPF-" "EGEIGVSPRVKDALSR") self.assertEqual(alignments[0][1].id, "gi|152973457|ref|YP_001338508.1|") self.assertEqual(alignments[0][1].annotations["original_length"], 931) self.assertEqual(len(alignments[1]), 2) self.assertEqual(alignments[1].get_alignment_length(), 64) self.assertEqual(alignments[1][0].seq, "AAECGKTVSGFLRAAALGKKVNS" "LTDDRVLKEV-MRLGALQKKLFI" "DGKRVGDREYAEVLIAIT") self.assertEqual(alignments[1][0].id, "gi|10955263|ref|NP_052604.1|") self.assertEqual(alignments[1][0].annotations["original_length"], 107) self.assertEqual(alignments[1][1].seq, "ASRQGCTVGG--KMDSVQDKASD" "KDKERVMKNINIMWNALSKNRLF" "DG----NKELKEFIMTLT") self.assertEqual(alignments[1][1].id, "gi|152973588|ref|YP_001338639.1|") self.assertEqual(alignments[1][1].annotations["original_length"], 459) self.assertEqual(len(alignments[2]), 2) self.assertEqual(alignments[2].get_alignment_length(), 45) self.assertEqual(alignments[2][0].seq, "EIRKRAAECGKTVSGFLRAAA--" "---LGKKVNSLTDDRVLKEVMR") self.assertEqual(alignments[2][0].id, "gi|10955263|ref|NP_052604.1|") self.assertEqual(alignments[2][0].annotations["original_length"], 107) self.assertEqual(alignments[2][1].seq, "ELVKLIADMGISVRALLRKNVEP" "YEELGLEEDKFTDDQLIDFMLQ") self.assertEqual(alignments[2][1].id, "gi|152973480|ref|YP_001338531.1|") self.assertEqual(alignments[2][1].annotations["original_length"], 141) self.assertEqual(len(alignments[3]), 2) self.assertEqual(alignments[3].get_alignment_length(), 38) self.assertEqual(alignments[3][0].seq, "MKKDKKYQIEAIKNKDKTLFIVY" "ATDIYSPSEFFSKIE") self.assertEqual(alignments[3][0].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[3][0].annotations["original_length"], 126) self.assertEqual(alignments[3][1].seq, "IKKDLGVSFLKLKNREKTLIVDA" "LKKKYPVAELLSVLQ") self.assertEqual(alignments[3][1].id, "gi|152973462|ref|YP_001338513.1|") self.assertEqual(alignments[3][1].annotations["original_length"], 101) self.assertEqual(len(alignments[4]), 2) self.assertEqual(alignments[4].get_alignment_length(), 11) self.assertEqual(alignments[4][0].seq, "FFDLIIPNGGK") self.assertEqual(alignments[4][0].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[4][0].annotations["original_length"], 126) self.assertEqual(alignments[4][1].seq, "FFDLVIENPGK") self.assertEqual(alignments[4][1].id, "gi|152973509|ref|YP_001338560.1|") self.assertEqual(alignments[4][1].annotations["original_length"], 448) self.assertEqual(len(alignments[5]), 2) self.assertEqual(alignments[5].get_alignment_length(), 40) self.assertEqual(alignments[5][0].seq, "DKTLFIVYATDIYSPSE-FFSKI" "ESDLKKKKSKGD-VFFD") self.assertEqual(alignments[5][0].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[5][0].annotations["original_length"], 126) self.assertEqual(alignments[5][1].seq, "ESVVFILMAGFAMSVCYLFFSVL" "EKVINARKSKDESIYHD") self.assertEqual(alignments[5][1].id, "gi|152973581|ref|YP_001338632.1|") self.assertEqual(alignments[5][1].annotations["original_length"], 84) self.assertEqual(len(alignments[6]), 2) self.assertEqual(alignments[6].get_alignment_length(), 30) self.assertEqual(alignments[6][0].seq, "ASFFKKNFDKINVNLLSKATSFA" "LKKGIPI") self.assertEqual(alignments[6][0].id, "gi|10955264|ref|NP_052605.1|") self.assertEqual(alignments[6][0].annotations["original_length"], 126) self.assertEqual(alignments[6][1].seq, "ASFSKEEQDKVAVDKVAADVAWQ" "ERMNKPV") self.assertEqual(alignments[6][1].id, "gi|152973536|ref|YP_001338587.1|") self.assertEqual(alignments[6][1].annotations["original_length"], 84) self.assertEqual(len(alignments[7]), 2) self.assertEqual(alignments[7].get_alignment_length(), 43) self.assertEqual(alignments[7][0].seq, "SELHSKLPKSIDKIHEDIKKQLS" "C-SLIMKKIDVEMEDYSTYC") self.assertEqual(alignments[7][0].id, "gi|10955265|ref|NP_052606.1|") self.assertEqual(alignments[7][0].annotations["original_length"], 346) self.assertEqual(alignments[7][1].seq, "SRINSDVARRIPGIHRDPKDRLS" "SLKQVEEALDMLISSHGEYC") self.assertEqual(alignments[7][1].id, "gi|152973545|ref|YP_001338596.1|") self.assertEqual(alignments[7][1].annotations["original_length"], 242) self.assertEqual(len(alignments[8]), 2) self.assertEqual(alignments[8].get_alignment_length(), 64) self.assertEqual(alignments[8][0].seq, "ISGTYKGIDFLIKLMPSGGNTTI" "GRASGQNNTYFDEIALIIKENCL" "Y--SDTKNFEYTIPKFSD") self.assertEqual(alignments[8][0].id, "gi|10955265|ref|NP_052606.1|") self.assertEqual(alignments[8][0].annotations["original_length"], 346) self.assertEqual(alignments[8][1].seq, "IDGVITAFD-LRTGMNISKDKVV" "AQIQGMDPVW---ISAAVPESIA" "YLLKDTSQFEISVPAYPD") self.assertEqual(alignments[8][1].id, "gi|152973505|ref|YP_001338556.1|") self.assertEqual(alignments[8][1].annotations["original_length"], 430) def test_output008(self): """Check output008.m10 file.""" fasta_file = 'Fasta/output008.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 12) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 65) self.assertEqual(alignments[0][0].seq, "LQHRHPHQQQQQQQQQQQQQQQQ" "QQQQQQQQQQQH---HHHHHHHL" "LQDAYMQQYQHATQQQQML") self.assertEqual(alignments[0][0].id, "sp|Q9NSY1|BMP2K_HUMAN") self.assertEqual(alignments[0][0].annotations["original_length"], 1161) self.assertEqual(alignments[0][1].seq, "IPHQLPHALRHRPAQEAAHASQL" "HPAQPGCGQPLHGLWRLHHHPVY" "LYAWILRLRGHGMQSGGLL") self.assertEqual(alignments[0][1].id, "gi|283855822|gb|GQ290312.1|") self.assertEqual(alignments[0][1].annotations["original_length"], 983) self.assertEqual(len(alignments[1]), 2) self.assertEqual(alignments[1].get_alignment_length(), 201) self.assertEqual(alignments[1][0].seq, "GPEIL---LGQ-GPPQQPPQQHR" "VLQQLQQGDWRLQQLH-------" "LQHRHPHQQQQQQQQQQQQQQQQ" "QQQQQQQQQQQH-----HHHHHH" "-HLLQDAYMQQYQHATQQQQMLQ" "QQF-LMHSVYQPQPSASQYPTMM" "PQYQQAFFQQQMLAQHQPSQQQA" "SPEYLTSPQEFSPALVSYTSSLP" "A-QVGTIMDSSYSANRS") self.assertEqual(alignments[1][0].id, "sp|Q9NSY1|BMP2K_HUMAN") self.assertEqual(alignments[1][0].annotations["original_length"], 1161) self.assertEqual(alignments[1][1].seq, "GPELLRALLQQNGCGTQPLRVPT" "VLPG*AMAVLHAGRLHVPAHRAW" "LPHQLPHALRHGPAQEAAHASQL" "HPAQPGRG*PLHGLRWLHHHPLH" "/PLCMDTLSLGPQDAIWRASLPH" "WAVKLPCGLWWSWPLSGTWWCVS" "P*ATSA------LGRTMP*WASL" "SPGSWHWPALHPPSLVGPGTSLK" "ACSVHAGSTTTHSSQKS") self.assertEqual(alignments[1][1].id, "gi|57163782|ref|NM_001009242.1|") self.assertEqual(alignments[1][1].annotations["original_length"], 1047) self.assertEqual(len(alignments[2]), 2) self.assertEqual(alignments[2].get_alignment_length(), 348) self.assertEqual(alignments[2][0].seq, "MNGTEGPNFYVPFSNATGVVRSP" "FEYPQYYLAEPWQFSMLAAYMFL" "LIVLGFPINFLTLYVTVQHKKLR" "TPLNYILLNLAVADLFMVLGGFT" "STLYTSLHGYFVFGPTGCNLEGF" "FATLGGEIALWSLVVLAIERYVV" "VCKPMSNFRFGENHAIMGVAFTW" "VMALACAAPPLAGWSRYIPEGLQ" "CSCGIDYYTLKPEVNNESFVIYM" "FVVHFTIPMIIIFFCYGQLVFTV" "KEAAAQQQESATTQKAEKEVTRM" "VIIMVIAFLICWVPYASVAFYIF" "THQGSNFGPIFMTIPAFFAKSAA" "IYNPVIYIMMNKQFRNCMLTTIC" "CGKNPLGDDEASATVSKTETSQV" "APA") self.assertEqual(alignments[2][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[2][0].annotations["original_length"], 348) self.assertEqual(alignments[2][1].seq, "MNGTEGPNFYVPFSNKTGVVRSP" "FEYPQYYLAEPWQFSMLAAYMFL" "LIVLGFPINFLTLYVTVQHKKLR" "TPLNYILLNLAVADLFMVFGGFT" "TTLYTSLHGYFVFGPTGCNLEGF" "FATLGGEIALWSLVVLAIERYVV" "VCKPMSNFRFGENHAIMGVAFTW" "VMALACAAPPLVGWSRYIPEGMQ" "CSCGIDYYTLKPEVNNESFVIYM" "FVVHFTIPMIVIFFCYGQLVFTV" "KEAAAQQQESATTQKAEKEVTRM" "VIIMVIAFLICWVPYASVAFYIF" "THQGSNFGPIFMTLPAFFAKSSS" "IYNPVIYIMMNKQFRNCMLTTLC" "CGKNPLGDDEASTTGSKTETSQV" "APA") self.assertEqual(alignments[2][1].id, "gi|57163782|ref|NM_001009242.1|") self.assertEqual(alignments[2][1].annotations["original_length"], 1047) self.assertEqual(len(alignments[3]), 2) self.assertEqual(alignments[3].get_alignment_length(), 348) self.assertEqual(alignments[3][0].seq, "MNGTEGPNFYVPFSNATGVVRSP" "FEYPQYYLAEPWQFSMLAAYMFL" "LIVLGFPINFLTLYVTVQHKKLR" "TPLNYILLNLAVADLFMVLGGFT" "STLYTSLHGYFVFGPTGCNLEGF" "FATLGGEIALWSLVVLAIERYVV" "VCKPMSNFRFGENHAIMGVAFTW" "VMALACAAPPLAGWSRYIPEGLQ" "CSCGIDYYTLKPEVNNESFVIYM" "FVVHFTIPMIIIFFCYGQLVFTV" "KEAAAQQQESATTQKAEKEVTRM" "VIIMVIAFLICWVPYASVAFYIF" "THQGSNFGPIFMTIPAFFAKSAA" "IYNPVIYIMMNKQFRNCMLTTIC" "CGKNPLGDDEASATVSKTETSQV" "APA") self.assertEqual(alignments[3][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[3][0].annotations["original_length"], 348) self.assertEqual(alignments[3][1].seq, "MNGTEGPNFYVPFSNKTGVVRSP" "FEAPQYYLAEPWQFSMLAAYMFL" "LIMLGFPINFLTLYVTVQHKKLR" "TPLNYILLNLAVADLFMVFGGFT" "TTLYTSLHGYFVFGPTGCNLEGF" "FATLGGEIALWSLVVLAIERYVV" "VCKPMSNFRFGENHAIMGVAFTW" "VMALACAAPPLVGWSRYIPEGMQ" "CSCGIDYYTPHEETNNESFVIYM" "FVVHFIIPLIVIFFCYGQLVFTV" "KEAAAQQQESATTQKAEKEVTRM" "VIIMVIAFLICWLPYAGVAFYIF" "THQGSDFGPIFMTIPAFFAKTSA" "VYNPVIYIMMNKQFRNCMVTTLC" "CGKNPLGDDEASTTVSKTETSQV" "APA") self.assertEqual(alignments[3][1].id, "gi|18148870|dbj|AB062417.1|") self.assertEqual(alignments[3][1].annotations["original_length"], 1047) self.assertEqual(len(alignments[4]), 2) self.assertEqual(alignments[4].get_alignment_length(), 326) self.assertEqual(alignments[4][0].seq, "VPFSNATGVVRSPFEYPQYYLAE" "PWQFSMLAAYMFLLIVLGFPINF" "LTLYVTVQHKKLRTPLNYILLNL" "AVADLFMVLGGFTSTLYTSLHGY" "FVFGPTGCNLEGFFATLGGEIAL" "WSLVVLAIERYVVVCKPMSNFRF" "GENHAIMGVAFTWVMALACAAPP" "LAGWSRYIPEGLQCSCGIDYYTL" "KPEVNNESFVIYMFVVHFTIPMI" "IIFFCYGQLVFTVKEAAAQQQES" "ATTQKAEKEVTRMVIIMVIAFLI" "CWVPYASVAFYIFTHQGSNFGPI" "FMTIPAFFAKSAAIYNPVIYIMM" "NKQFRNCMLTTICCGKNPLGDDE" "ASAT") self.assertEqual(alignments[4][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[4][0].annotations["original_length"], 348) self.assertEqual(alignments[4][1].seq, "VPFSNKTGVVRSPFEYPQYYLAE" "PWQFSMLAAYMFLLIVLGFPINF" "LTLYVTVQHKKLRTPLNYILLNL" "AVANLFMVFGGFTTTLYTSMHGY" "FVFGATGCNLEGFFATLGGEIAL" "WSLVVLAIERYVVVCKPMSNFRF" "GENHAIMGLAFTWVMALACAAPP" "LAGWSRYIPEGMQCSCGIDYYTL" "KPEVNNESFVIYMFVVHFTIPMI" "VIFFCYGQLVFTVKEAAAQQQES" "ATTQKAEKEVTRMVIIMVVAFLI" "CWLPYASVAFYIFTHQGSNFGPV" "FMTIPAFFAKSSSIYNPVIYIMM" "NKQFRNCMLTTLCCGKNPLGDDE" "ASTT") self.assertEqual(alignments[4][1].id, "gi|283855822|gb|GQ290312.1|") self.assertEqual(alignments[4][1].annotations["original_length"], 983) self.assertEqual(len(alignments[5]), 2) self.assertEqual(alignments[5].get_alignment_length(), 354) self.assertEqual(alignments[5][0].seq, "MNGTEGPNFYVPFSNATGVVRSP" "FEYPQYYLAEPWQFSMLAAYMFL" "LIVLGFPINFLTLYVTVQHKKLR" "TPLNYILLNLAVADLFMVLGGFT" "STLYTSLHGYFVFGPTGCNLEGF" "FATLGGEIALWSLVVLAIERYVV" "VCKPMSNFRFGENHAIMGVAFTW" "VMALACAAPPLAGWSRYIPEGLQ" "CSCGIDYYTLKPEVNNESFVIYM" "FVVHFTIPMIIIFFCYGQLVFTV" "KEAAAQQQESATTQKAEKEVTRM" "VIIMVIAFLICWVPYASVAFYIF" "THQGSNFGPIFMTIPAFFAKSAA" "IYNPVIYIMMNKQFRNCMLTTIC" "CGKNPLGDDEAS-ATVSKTE---" "--TSQVAPA") self.assertEqual(alignments[5][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[5][0].annotations["original_length"], 348) self.assertEqual(alignments[5][1].seq, "MNGTEGPNFYIPMSNKTGVVRSP" "FEYPQYYLAEPWQYSILCAYMFL" "LILLGFPINFMTLYVTIQHKKLR" "TPLNYILLNLAFANHFMVLCGFT" "VTMYSSMNGYFILGATGCYVEGF" "FATLGGEIALWSLVVLAIERYVV" "VCKPMSNFRFSENHAVMGVAFTW" "IMALSCAVPPLLGWSRYIPEGMQ" "CSCGVDYYTLKPEVNNESFVIYM" "FVVHFTIPLIIIFFCYGRLVCTV" "KEAAAQQQESATTQKAEKEVTRM" "VIIMVVFFLICWVPYASVAFFIF" "SNQGSEFGPIFMTVPAFFAKSSS" "IYNPVIYIMLNKQFRNCMITTLC" "CGKNPFGEDDASSAATSKTEASS" "VSSSQVSPA") self.assertEqual(alignments[5][1].id, "gi|2734705|gb|U59921.1|BBU59921") self.assertEqual(alignments[5][1].annotations["original_length"], 1574) self.assertEqual(len(alignments[6]), 2) self.assertEqual(alignments[6].get_alignment_length(), 347) self.assertEqual(alignments[6][0].seq, "MNGTEGPNFYVPFSNATGVVRSP" "FEYPQYYLAEPWQFSMLAAYMFL" "LIVLGFPINFLTLYVTVQHKKLR" "TPLNYILLNLAVADLFMVLGGFT" "STLYTSLHGYFVFGPTGCNLEGF" "FATLGGEIALWSLVVLAIERYVV" "VCKPMSNFRFGENHAIMGVAFTW" "VMALACAAPPLAGWSRYIPEGLQ" "CSCGIDYYTLKPEVNNESFVIYM" "FVVHFTIPMIIIFFCYGQLVFTV" "KEAAAQQQESATTQKAEKEVTRM" "VIIMVIAFLICWVPYASVAFYIF" "THQGSNFGPIFMTIPAFFAKSAA" "IYNPVIYIMMNKQFRNCMLTTIC" "CGKNPLGD-DEASATVSKTETSQ" "VA") self.assertEqual(alignments[6][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[6][0].annotations["original_length"], 348) self.assertEqual(alignments[6][1].seq, "MNGTEGPNFYIPMSNATGVVRSP" "FEYPQYYLAEPWAFSALSAYMFF" "LIIAGFPINFLTLYVTIEHKKLR" "TPLNYILLNLAVADLFMVFGGFT" "TTMYTSMHGYFVFGPTGCNIEGF" "FATLGGEIALWCLVVLAIERWMV" "VCKPVTNFRFGESHAIMGVMVTW" "TMALACALPPLFGWSRYIPEGLQ" "CSCGIDYYTRAPGINNESFVIYM" "FTCHFSIPLAVISFCYGRLVCTV" "KEAAAQQQESETTQRAEREVTRM" "VVIMVISFLVCWVPYASVAWYIF" "THQGSTFGPIFMTIPSFFAKSSA" "LYNPMIYICMNKQFRHCMITTLC" "CGKNPFEEEDGASATSSKTEASS" "VS") self.assertEqual(alignments[6][1].id, "gi|12583664|dbj|AB043817.1|") self.assertEqual(alignments[6][1].annotations["original_length"], 1344) self.assertEqual(len(alignments[7]), 2) self.assertEqual(alignments[7].get_alignment_length(), 111) self.assertEqual(alignments[7][0].seq, "VPFSNATGVVRSPFEYPQYYLAE" "PWQFSMLAAYMFLLIVLGFPINF" "LTLYVTVQHKKLRTPLNYILLNL" "AVADLFMVLGGFTSTLYTSLHGY" "FVFGPTGCNLEGFFATLGG") self.assertEqual(alignments[7][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[7][0].annotations["original_length"], 348) self.assertEqual(alignments[7][1].seq, "VPFSNKTGVVRSPFEHPQYYLAE" "PWQFSMLAAYMFLLIVLGFPINF" "LTLYVTVQHKKLRTPLNYILLNL" "AVADLFMVFGGFTTTLYTSLHGY" "FVFGPTGCNLEGFFATLGG") self.assertEqual(alignments[7][1].id, "gi|283855845|gb|GQ290303.1|") self.assertEqual(alignments[7][1].annotations["original_length"], 4301) self.assertEqual(len(alignments[8]), 2) self.assertEqual(alignments[8].get_alignment_length(), 172) self.assertEqual(alignments[8][0].seq, "RYIPEGLQCSCGIDYYTLKPEVN" "NESFVIYMFVVHFTIPMIIIFFC" "YGQLVFTVKE-------------" "-----------------------" "AAAQQQESATTQKAEKEVTRMVI" "IMVIAFLICWVPYASVAFYIFTH" "QGSNFGPIFMTIPAFFAKSAAIY" "NPVIYIMMNKQ") self.assertEqual(alignments[8][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[8][0].annotations["original_length"], 348) self.assertEqual(alignments[8][1].seq, "RYIPEGMQCSCGIDYYTLKPEVN" "NESFVIYMFVVHFTIPMIVIFFC" "YGQLVFTVKEVRSCVGHWGHAH*" "VNGAQLHSQSCHSLDT*PCVPA\\" "AAAQQQESATTQKAEKEVTRMVI" "IMVIAFLICWLPYAGVAFYIFTH" "QGSNFGPIFMTLPAFFAKSSSIY" "NPVIYIMMNKQ") self.assertEqual(alignments[8][1].id, "gi|283855845|gb|GQ290303.1|") self.assertEqual(alignments[8][1].annotations["original_length"], 4301) self.assertEqual(len(alignments[9]), 2) self.assertEqual(alignments[9].get_alignment_length(), 73) self.assertEqual(alignments[9][0].seq, "LGGEIALWSLVVLAIERYVVVCK" "PMSNFRFGENHAIMGVAFTWVMA" "LACAAPPLAGWSR--YIPEGLQC" "SCGI") self.assertEqual(alignments[9][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[9][0].annotations["original_length"], 348) self.assertEqual(alignments[9][1].seq, "LAGEIALWSLVVLAIERYVVVCK" "PMSNFRFGENHAIMGLALTWVMA" "LACAAPPLVGWSR*WH*TEG-KC" "L*GL") self.assertEqual(alignments[9][1].id, "gi|283855845|gb|GQ290303.1|") self.assertEqual(alignments[9][1].annotations["original_length"], 4301) self.assertEqual(len(alignments[10]), 2) self.assertEqual(alignments[10].get_alignment_length(), 30) self.assertEqual(alignments[10][0].seq, "IMMNKQFRNCMLTTICCGKNPL" "GDDEASAT") self.assertEqual(alignments[10][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[10][0].annotations["original_length"], 348) self.assertEqual(alignments[10][1].seq, "MLLAFQFRNCMLTTLCCGKNPL" "GDDEASTT") self.assertEqual(alignments[10][1].id, "gi|283855845|gb|GQ290303.1|") self.assertEqual(alignments[10][1].annotations["original_length"], 4301) self.assertEqual(len(alignments[11]), 2) self.assertEqual(alignments[11].get_alignment_length(), 31) self.assertEqual(alignments[11][0].seq, "AQQQESATTQKAEKEVTRMVIIMVIAFLICW") self.assertEqual(alignments[11][0].id, "sp|P08100|OPSD_HUMAN") self.assertEqual(alignments[11][0].annotations["original_length"], 348) self.assertEqual(alignments[11][1].seq, "SQQIRNATTMMMTMRVTSFSAFW" "VVADSCCW") self.assertEqual(alignments[11][1].id, "gi|283855822|gb|GQ290312.1|") self.assertEqual(alignments[11][1].annotations["original_length"], 983) def test_output009(self): """Check output009.m10 file.""" fasta_file = 'Fasta/output009.m10' with open(fasta_file, "r") as handle: alignments = list(FastaIO.FastaM10Iterator(handle)) self.assertEqual(len(alignments), 7) self.assertEqual(len(alignments[0]), 2) self.assertEqual(alignments[0].get_alignment_length(), 22) self.assertEqual(alignments[0][0].seq, "TGATGTTCTGTTTCTAAAACAG") self.assertEqual(alignments[0][0].id, "gi|255708421:1-99") self.assertEqual(alignments[0][0].annotations["original_length"], 99) self.assertEqual(alignments[0][1].seq, "TGATTTTTTTTGTCTAAAACAG") self.assertEqual(alignments[0][1].id, "gi|23308614|ref|NM_152952.1|") self.assertEqual(alignments[0][1].annotations["original_length"], 5188) self.assertEqual(len(alignments[1]), 2) self.assertEqual(alignments[1].get_alignment_length(), 14) self.assertEqual(alignments[1][0].seq, "AGAAGGAAAAAAAA") self.assertEqual(alignments[1][0].id, "gi|156718121:2361-2376") self.assertEqual(alignments[1][0].annotations["original_length"], 16) self.assertEqual(alignments[1][1].seq, "AGAACTAAAAAAAA") self.assertEqual(alignments[1][1].id, "gi|47271416|ref|NM_131257.2|") self.assertEqual(alignments[1][1].annotations["original_length"], 597) self.assertEqual(len(alignments[2]), 2) self.assertEqual(alignments[2].get_alignment_length(), 14) self.assertEqual(alignments[2][0].seq, "AGAAGGAAAAAAAA") self.assertEqual(alignments[2][0].id, "gi|156718121:2361-2376") self.assertEqual(alignments[2][0].annotations["original_length"], 16) self.assertEqual(alignments[2][1].seq, "AGAAGGTATAAAAA") self.assertEqual(alignments[2][1].id, "gi|332859474|ref|XM_001156938.2|") self.assertEqual(alignments[2][1].annotations["original_length"], 762) self.assertEqual(len(alignments[3]), 2) self.assertEqual(alignments[3].get_alignment_length(), 14) self.assertEqual(alignments[3][0].seq, "TTTTTTTCCTTCTT") self.assertEqual(alignments[3][0].id, "gi|156718121:2361-2376") self.assertEqual(alignments[3][0].annotations["original_length"], 16) self.assertEqual(alignments[3][1].seq, "TTTTTTTACATCTT") self.assertEqual(alignments[3][1].id, "gi|332211534|ref|XM_003254825.1|") self.assertEqual(alignments[3][1].annotations["original_length"], 805) self.assertEqual(len(alignments[4]), 2) self.assertEqual(alignments[4].get_alignment_length(), 14) self.assertEqual(alignments[4][0].seq, "AAGAAGGAAAAAAA") self.assertEqual(alignments[4][0].id, "gi|156718121:2361-2376") self.assertEqual(alignments[4][0].annotations["original_length"], 16) self.assertEqual(alignments[4][1].seq, "AATAAGTAAAAAAA") self.assertEqual(alignments[4][1].id, "gi|23308614|ref|NM_152952.1|") self.assertEqual(alignments[4][1].annotations["original_length"], 5188) self.assertEqual(len(alignments[5]), 2) self.assertEqual(alignments[5].get_alignment_length(), 14) self.assertEqual(alignments[5][0].seq, "TTTTTTTCCTTCTT") self.assertEqual(alignments[5][0].id, "gi|156718121:2361-2376") self.assertEqual(alignments[5][0].annotations["original_length"], 16) self.assertEqual(alignments[5][1].seq, "TTTTTTTACATCTT") self.assertEqual(alignments[5][1].id, "gi|297689475|ref|XM_002822130.1|") self.assertEqual(alignments[5][1].annotations["original_length"], 1158) self.assertEqual(len(alignments[6]), 2) self.assertEqual(alignments[6].get_alignment_length(), 14) self.assertEqual(alignments[6][0].seq, "AAGAAGGAAAAAAA") self.assertEqual(alignments[6][0].id, "gi|156718121:2361-2376") self.assertEqual(alignments[6][0].annotations["original_length"], 16) self.assertEqual(alignments[6][1].seq, "AAGAAGGTAAAAGA") self.assertEqual(alignments[6][1].id, "gi|297689475|ref|XM_002822130.1|") self.assertEqual(alignments[6][1].annotations["original_length"], 1158) if __name__ == '__main__': runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)