# Copyright 2005 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. import os import unittest from Bio.Blast import NCBIXML E_VALUE_THRESH = 1e-10 class TestNCBIXML(unittest.TestCase): def test_xbt001(self): "Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xbt001)" filename = 'xbt001.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() alignments = record.alignments self.assertEqual(len(alignments), 212) self.assertEqual(record.query_id, "gi|49176427|ref|NP_418280.3|") self.assertEqual(sum([len(a.hsps) for a in alignments]), 212) alignment = alignments[0] self.assertEqual(alignment.title[:50], "gi|49176427|ref|NP_418280.3| component of Sec-inde") self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 4.20576e-46) self.assertEqual(hsp.query[:75], "MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") self.assertEqual(hsp.match[:75], "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") self.assertEqual(hsp.sbjct[:75], "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") alignment = alignments[1] self.assertEqual(alignment.title[:50], "gi|15804428|ref|NP_290468.1| twin arginine translo") self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.72609e-45) self.assertEqual(hsp.query[:75], "MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") self.assertEqual(hsp.match[:75], "MRLCLIIIYHR TCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") self.assertEqual(hsp.sbjct[:75], "MRLCLIIIYHRXTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") alignment = alignments[2] self.assertEqual(alignment.title[:50], "gi|74314349|ref|YP_312768.1| hypothetical protein ") self.assertEqual(alignment.length, 103) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.72609e-45) self.assertEqual(hsp.query[:75], "MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") self.assertEqual(hsp.match[:75], "MR CLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") self.assertEqual(hsp.sbjct[:75], "MRPCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA") alignment = alignments[3] self.assertEqual(alignment.title[:50], "gi|75256240|ref|ZP_00727918.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 6.0872e-37) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") alignment = alignments[4] self.assertEqual(alignment.title[:50], "gi|148236|gb|AAA67633.1| o261 [Escherichia coli]") self.assertEqual(alignment.length, 261) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 6.74582e-28) self.assertEqual(hsp.query[:75], "FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA") self.assertEqual(hsp.match[:75], "FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA") self.assertEqual(hsp.sbjct[:75], "FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA") alignment = alignments[5] self.assertEqual(alignment.title[:50], "gi|29143650|ref|NP_806992.1| sec-independent prote") self.assertEqual(alignment.length, 84) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 4.37251e-27) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLI+AVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDD+ KQDKTSQDADFTAK+IADKQ +") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIVAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDDAKQDKTSQDADFTAKSIADKQG-----E") alignment = alignments[6] self.assertEqual(alignment.title[:50], "gi|49609685|emb|CAG73118.1| sec-independent protei") self.assertEqual(alignment.length, 86) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 4.10205e-17) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEP--KQDKTSQDADFTAKTIADKQADTNQ") self.assertEqual(hsp.match[:75], "MGGIS+W LLIIAVIV+LLFGT KL ++GSDLGASIKGFKKAM DD+P DK DADF+ K+IAD Q+D ") self.assertEqual(hsp.sbjct[:75], "MGGISLWNLLIIAVIVILLFGTNKLRTLGSDLGASIKGFKKAMGDDQPSTNADKAQPDADFSTKSIADNQSD---") alignment = alignments[7] self.assertEqual(alignment.title[:50], "gi|37528238|ref|NP_931583.1| Sec-independent prote") self.assertEqual(alignment.length, 86) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.25087e-15) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDD-EPKQ-DKTSQDADFTAKTIADKQADTNQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGT KL ++GSDLGASIKGFKKA+ DD +P+Q KTS DADF K I +KQ+ ") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTNKLRTLGSDLGASIKGFKKAIGDDNQPQQAQKTSSDADFETKNITEKQS----") alignment = alignments[8] self.assertEqual(alignment.title[:50], "gi|59710656|ref|YP_203432.1| Sec-independent prote") self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 5.01441e-15) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIAVI+VLLFGTKKL +GSDLG+++KGFKKA+S+DEP ++ +DADF + + K+A+T ++Q") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIAVIIVLLFGTKKLRGVGSDLGSAVKGFKKAISEDEPAKE-AKKDADFVPQNLEKKEAETVEKQ") alignment = alignments[9] self.assertEqual(alignment.title[:50], "gi|54307340|ref|YP_128360.1| putative TatA protein") self.assertEqual(alignment.length, 87) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 7.2408e-14) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE--PKQDKTSQDADFTAKTIADKQADTNQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIA+I+VLLFGTKKL S+G DLG+++KGFKKA+ D+E K+D T DADF KT++ ++ + ") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIALIIVLLFGTKKLRSLGGDLGSAVKGFKKAIGDEELTVKKDNTEADADFEQKTLSKEEQQSED") alignment = alignments[10] self.assertEqual(alignment.title[:50], "gi|45437890|gb|AAS63439.1| Sec-independent protein") self.assertEqual(alignment.length, 88) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 1.61308e-13) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE----PKQDKTSQDADFTAKTIADKQADT") self.assertEqual(hsp.match[:75], "MG I QLLIIAVIVVLLFGT KL ++GSDLGASIKGFKKAM DD DKTS DADF AK+I +KQ ") self.assertEqual(hsp.sbjct[:75], "MGSIGWAQLLIIAVIVVLLFGTNKLRTLGSDLGASIKGFKKAMGDDSQTPPTNVDKTSNDADF-AKSITEKQ---") alignment = alignments[11] self.assertEqual(alignment.title[:50], "gi|75856473|ref|ZP_00764101.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.10675e-13) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGIS+WQLLIIAVIVVLLFGTKKL IG DLG ++KGFKKAMS+DEP K +DADF K++ ++Q +++") self.assertEqual(hsp.sbjct[:75], "MGGISVWQLLIIAVIVVLLFGTKKLRGIGGDLGGAVKGFKKAMSEDEPA--KNDKDADFEPKSLEEQQ----KKE") alignment = alignments[12] self.assertEqual(alignment.title[:50], "gi|75829371|ref|ZP_00758676.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.7515e-13) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG+++KGFKKAMS++E +DADF K N EQ") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGSAVKGFKKAMSEEESNSAANQKDADFETK---------NLEQ") alignment = alignments[13] self.assertEqual(alignment.title[:50], "gi|75820019|ref|ZP_00750077.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.59357e-13) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG+++KGFKKAMS++E +DADF K N EQ") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGSAVKGFKKAMSEEESNSAANQKDADFETK---------NLEQ") alignment = alignments[14] self.assertEqual(alignment.title[:50], "gi|28896872|ref|NP_796477.1| TatA protein [Vibrio ") self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.32928e-12) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGIS+WQLLIIAVIVVLLFGTKKL IG DLG+++KGFKKAMSD++ K +DADF K++ +Q Q++") self.assertEqual(hsp.sbjct[:75], "MGGISVWQLLIIAVIVVLLFGTKKLRGIGGDLGSAVKGFKKAMSDED--SAKNEKDADFEPKSLEKQQ----QKE") alignment = alignments[15] self.assertEqual(alignment.title[:50], "gi|27364353|ref|NP_759881.1| Sec-independent prote") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.97316e-12) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG +IKGFKKAM+++E ++ +DADF K++ + +Q") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGGAIKGFKKAMNEEESEK----KDADFEPKSL-----EQQSKQ") alignment = alignments[16] self.assertEqual(alignment.title[:50], "gi|37678364|ref|NP_932973.1| Sec-independent prote") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.97316e-12) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG +IKGFKKAM+++E ++ +DADF K++ + +Q") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGGAIKGFKKAMNEEESEK----KDADFEPKSL-----EQQNKQ") alignment = alignments[17] self.assertEqual(alignment.title[:50], "gi|71277787|ref|YP_266931.1| Sec-independent prote") self.assertEqual(alignment.length, 85) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.97316e-12) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGI IWQL+I+AVIVVLLFGTKKL +IG DLG++IKGFK A+ +D K+ K S A+ T+ T+AD T +E ") self.assertEqual(hsp.sbjct[:75], "MGGIGIWQLVIVAVIVVLLFGTKKLRNIGGDLGSAIKGFKSAIGED--KEQKNS--AEKTSDTLADSSKSTTEEV") alignment = alignments[18] self.assertEqual(alignment.title[:50], "gi|68541995|ref|ZP_00581733.1| Twin-arginine trans") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.57533e-11) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKT---IADKQADTN") self.assertEqual(hsp.match[:75], "MGGISIWQLLI+A+IVVLLFGTKKL S+G DLG ++KGFK AMS +E K+ +A TA+T +K+ ++N") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIVALIVVLLFGTKKLRSLGGDLGGAVKGFKNAMSSEEDKKALEDTEAAKTAQTTQQATEKKPESN") alignment = alignments[19] self.assertEqual(alignment.title[:50], "gi|77813363|ref|ZP_00812641.1| Twin-arginine trans") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 2.57533e-11) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKT---IADKQADTN") self.assertEqual(hsp.match[:75], "MGGISIWQLLIIA+IVVLLFGTKKL S+G DLG ++KGFK AMS +E K+ +A TA+T +K+ ++N") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIALIVVLLFGTKKLRSLGGDLGGAVKGFKNAMSSEEDKKALEDTEAAKTAQTTQQATEKKPESN") alignment = alignments[20] self.assertEqual(alignment.title[:50], "gi|52306607|gb|AAU37107.1| TatA protein [Mannheimi") self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.36348e-11) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLII I+VLLFGTKKL ++G+DLG S+KGFKKAM++DEPK DA+F + D+ A E+") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIVAIIVLLFGTKKLRTLGTDLGESVKGFKKAMNEDEPK------DAEFKSLN-KDESATAGSEK") alignment = alignments[21] self.assertEqual(alignment.title[:50], "gi|75429751|ref|ZP_00732413.1| sec-independent pro") self.assertEqual(alignment.length, 74) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 3.36348e-11) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLII IVVLLFGTKKL ++GSDLG S+KGFKKAM+ +EPK DA+F + A+ A T +E+") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIVAIVVLLFGTKKLRTLGSDLGESVKGFKKAMA-EEPK------DAEFKSLDKAENTAQTKKEE") alignment = alignments[22] self.assertEqual(alignment.title[:50], "gi|32033565|ref|ZP_00133892.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) hsp = alignment.hsps[0] self.assertTrue(hsp.expect, 7.49305e-11) self.assertEqual(hsp.query[:75], "MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQ") self.assertEqual(hsp.match[:75], "MGGISIWQLLII I+VLLFGTKKL ++G+DLG S+KGFKKAM+DD+ SQ D + + + K+A + +++") self.assertEqual(hsp.sbjct[:75], "MGGISIWQLLIIVAIIVLLFGTKKLRTLGTDLGESVKGFKKAMADDK------SQPQDASFEKVEAKEAASTEQK") alignment = alignments[23] self.assertEqual(alignment.title[:50], "gi|12722097|gb|AAK03773.1| unknown [Pasteurella mu") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[24] self.assertEqual(alignment.title[:50], "gi|68546478|ref|ZP_00586025.1| Twin-arginine trans") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[25] self.assertEqual(alignment.title[:50], "gi|33151888|ref|NP_873241.1| sec-independent prote") self.assertEqual(alignment.length, 74) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[26] self.assertEqual(alignment.title[:50], "gi|24375687|ref|NP_719730.1| Sec-independent prote") self.assertEqual(alignment.length, 88) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[27] self.assertEqual(alignment.title[:50], "gi|71278553|ref|YP_269744.1| Sec-independent prote") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[28] self.assertEqual(alignment.title[:50], "gi|69159855|gb|EAN71956.1| Twin-arginine transloca") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[29] self.assertEqual(alignment.title[:50], "gi|69949858|ref|ZP_00637822.1| Twin-arginine trans") self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[30] self.assertEqual(alignment.title[:50], "gi|48863844|ref|ZP_00317737.1| hypothetical protei") self.assertEqual(alignment.length, 83) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[31] self.assertEqual(alignment.title[:50], "gi|77361831|ref|YP_341406.1| twin-arginine translo") self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[32] self.assertEqual(alignment.title[:50], "gi|67676224|ref|ZP_00472975.1| Twin-arginine trans") self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[33] self.assertEqual(alignment.title[:50], "gi|74317722|ref|YP_315462.1| twin-arginine translo") self.assertEqual(alignment.length, 70) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[34] self.assertEqual(alignment.title[:50], "gi|77166504|ref|YP_345029.1| Twin-arginine translo") self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[35] self.assertEqual(alignment.title[:50], "gi|16128610|ref|NP_415160.1| component of Sec-inde") self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[36] self.assertEqual(alignment.title[:50], "gi|12831974|emb|CAC29147.1| TatA protein [Pseudomo") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[37] self.assertEqual(alignment.title[:50], "gi|32029972|ref|ZP_00132908.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[38] self.assertEqual(alignment.title[:50], "gi|455172|gb|AAA24073.1| ORF; putative") self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[39] self.assertEqual(alignment.title[:50], "gi|1224007|gb|AAA92108.1| ORF4") self.assertEqual(alignment.length, 192) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[40] self.assertEqual(alignment.title[:50], "gi|68056990|gb|AAX87243.1| Sec-independent protein") self.assertEqual(alignment.length, 95) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[41] self.assertEqual(alignment.title[:50], "gi|56461470|ref|YP_156751.1| Sec-independent prote") self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[42] self.assertEqual(alignment.title[:50], "gi|76793313|ref|ZP_00775802.1| Twin-arginine trans") self.assertEqual(alignment.length, 84) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[43] self.assertEqual(alignment.title[:50], "gi|42630489|ref|ZP_00156028.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[44] self.assertEqual(alignment.title[:50], "gi|1074302|pir||B64145 hypothetical protein HI0187") self.assertEqual(alignment.length, 109) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[45] self.assertEqual(alignment.title[:50], "gi|67641583|ref|ZP_00440359.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[46] self.assertEqual(alignment.title[:50], "gi|67545726|ref|ZP_00423646.1| Twin-arginine trans") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[47] self.assertEqual(alignment.title[:50], "gi|45435806|gb|AAS61363.1| sec-independent protein") self.assertEqual(alignment.length, 85) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[48] self.assertEqual(alignment.title[:50], "gi|49610761|emb|CAG74206.1| Sec-independent protei") self.assertEqual(alignment.length, 65) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[49] self.assertEqual(alignment.title[:50], "gi|67663266|ref|ZP_00460549.1| Twin-arginine trans") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[50] self.assertEqual(alignment.title[:50], "gi|33594634|ref|NP_882278.1| Sec-independent prote") self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[51] self.assertEqual(alignment.title[:50], "gi|46310681|ref|ZP_00211309.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[52] self.assertEqual(alignment.title[:50], "gi|58584031|ref|YP_203047.1| sec-independent prote") self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[53] self.assertEqual(alignment.title[:50], "gi|17429965|emb|CAD16649.1| PROBABLE SIGNAL PEPTID") self.assertEqual(alignment.length, 85) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[54] self.assertEqual(alignment.title[:50], "gi|47573371|ref|ZP_00243410.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[55] self.assertEqual(alignment.title[:50], "gi|16273687|ref|NP_438355.1| Sec-independent prote") self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[56] self.assertEqual(alignment.title[:50], "gi|73542784|ref|YP_297304.1| Twin-arginine translo") self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[57] self.assertEqual(alignment.title[:50], "gi|26987777|ref|NP_743202.1| Sec-independent prote") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[58] self.assertEqual(alignment.title[:50], "gi|29142636|ref|NP_805978.1| sec-independent prote") self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[59] self.assertEqual(alignment.title[:50], "gi|18389921|gb|AAL68797.1| TatA [Ralstonia eutroph") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[60] self.assertEqual(alignment.title[:50], "gi|48781637|ref|ZP_00278228.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[61] self.assertEqual(alignment.title[:50], "gi|77456610|ref|YP_346115.1| Twin-arginine translo") self.assertEqual(alignment.length, 92) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[62] self.assertEqual(alignment.title[:50], "gi|1684735|emb|CAA98158.1| ORF57 protein [Pseudomo") self.assertEqual(alignment.length, 57) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[63] self.assertEqual(alignment.title[:50], "gi|56476124|ref|YP_157713.1| Sec-independent prote") self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[64] self.assertEqual(alignment.title[:50], "gi|34496078|ref|NP_900293.1| Sec-independent prote") self.assertEqual(alignment.length, 68) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[65] self.assertEqual(alignment.title[:50], "gi|67848115|ref|ZP_00503233.1| Twin-arginine trans") self.assertEqual(alignment.length, 83) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[66] self.assertEqual(alignment.title[:50], "gi|26991692|ref|NP_747117.1| Sec-independent prote") self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[67] self.assertEqual(alignment.title[:50], "gi|15601293|ref|NP_232924.1| tatA protein [Vibrio ") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[68] self.assertEqual(alignment.title[:50], "gi|66770480|ref|YP_245242.1| sec-independent prote") self.assertEqual(alignment.length, 75) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[69] self.assertEqual(alignment.title[:50], "gi|53804435|ref|YP_113945.1| Sec-independent prote") self.assertEqual(alignment.length, 70) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[70] self.assertEqual(alignment.title[:50], "gi|75825357|ref|ZP_00754793.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[71] self.assertEqual(alignment.title[:50], "gi|71908987|ref|YP_286574.1| Twin-arginine translo") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[72] self.assertEqual(alignment.title[:50], "gi|68526571|gb|EAN49542.1| Twin-arginine transloca") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[73] self.assertEqual(alignment.title[:50], "gi|71736448|ref|YP_272670.1| sec-independent prote") self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[74] self.assertEqual(alignment.title[:50], "gi|56460344|ref|YP_155625.1| Sec-independent prote") self.assertEqual(alignment.length, 72) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[75] self.assertEqual(alignment.title[:50], "gi|68214708|ref|ZP_00566522.1| Twin-arginine trans") self.assertEqual(alignment.length, 72) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[76] self.assertEqual(alignment.title[:50], "gi|30248650|ref|NP_840720.1| mttA/Hcf106 family [N") self.assertEqual(alignment.length, 76) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[77] self.assertEqual(alignment.title[:50], "gi|75822907|ref|ZP_00752458.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[78] self.assertEqual(alignment.title[:50], "gi|70733926|ref|YP_257566.1| sec-independent prote") self.assertEqual(alignment.length, 93) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[79] self.assertEqual(alignment.title[:50], "gi|63254358|gb|AAY35454.1| Twin-arginine transloca") self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[80] self.assertEqual(alignment.title[:50], "gi|73354814|gb|AAZ75668.1| TatA [Pseudomonas syrin") self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[81] self.assertEqual(alignment.title[:50], "gi|50083761|ref|YP_045271.1| Sec-independent prote") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[82] self.assertEqual(alignment.title[:50], "gi|71548504|ref|ZP_00668728.1| Twin-arginine trans") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[83] self.assertEqual(alignment.title[:50], "gi|55247002|gb|EAL42253.1| ENSANGP00000028218 [Ano") self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[84] self.assertEqual(alignment.title[:50], "gi|50084688|ref|YP_046198.1| Sec-independent prote") self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[85] self.assertEqual(alignment.title[:50], "gi|28872267|ref|NP_794886.1| sec-independent prote") self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[86] self.assertEqual(alignment.title[:50], "gi|49082486|gb|AAT50643.1| PA5068 [synthetic const") self.assertEqual(alignment.length, 83) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[87] self.assertEqual(alignment.title[:50], "gi|53726598|ref|ZP_00141543.2| COG1826: Sec-indepe") self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[88] self.assertEqual(alignment.title[:50], "gi|68213616|ref|ZP_00565447.1| Twin-arginine trans") self.assertEqual(alignment.length, 54) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[89] self.assertEqual(alignment.title[:50], "gi|74023810|ref|ZP_00694377.1| Twin-arginine trans") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[90] self.assertEqual(alignment.title[:50], "gi|71066554|ref|YP_265281.1| twin-arginine translo") self.assertEqual(alignment.length, 87) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[91] self.assertEqual(alignment.title[:50], "gi|15611372|ref|NP_223023.1| hypothetical protein ") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[92] self.assertEqual(alignment.title[:50], "gi|13471183|ref|NP_102752.1| sec-independent prote") self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[93] self.assertEqual(alignment.title[:50], "gi|42523995|ref|NP_969375.1| twin-arginine-depende") self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[94] self.assertEqual(alignment.title[:50], "gi|67158086|ref|ZP_00419176.1| Twin-arginine trans") self.assertEqual(alignment.length, 85) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[95] self.assertEqual(alignment.title[:50], "gi|15644948|ref|NP_207118.1| conserved hypothetica") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[96] self.assertEqual(alignment.title[:50], "gi|13277311|emb|CAC34414.1| putative TatA protein ") self.assertEqual(alignment.length, 61) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[97] self.assertEqual(alignment.title[:50], "gi|54298906|ref|YP_125275.1| Putative TatA protein") self.assertEqual(alignment.length, 61) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[98] self.assertEqual(alignment.title[:50], "gi|71363513|ref|ZP_00654157.1| Twin-arginine trans") self.assertEqual(alignment.length, 94) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[99] self.assertEqual(alignment.title[:50], "gi|71362217|ref|ZP_00653377.1| Twin-arginine trans") self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[100] self.assertEqual(alignment.title[:50], "gi|27379862|ref|NP_771391.1| hypothetical protein ") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[101] self.assertEqual(alignment.title[:50], "gi|39935914|ref|NP_948190.1| putative sec-independ") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[102] self.assertEqual(alignment.title[:50], "gi|17935600|ref|NP_532390.1| SEC-independent prote") self.assertEqual(alignment.length, 70) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[103] self.assertEqual(alignment.title[:50], "gi|62289827|ref|YP_221620.1| Sec-independent prote") self.assertEqual(alignment.length, 72) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[104] self.assertEqual(alignment.title[:50], "gi|23347697|gb|AAN29810.1| Sec-independent protein") self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[105] self.assertEqual(alignment.title[:50], "gi|75675971|ref|YP_318392.1| twin-arginine translo") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[106] self.assertEqual(alignment.title[:50], "gi|69928230|ref|ZP_00625391.1| Twin-arginine trans") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[107] self.assertEqual(alignment.title[:50], "gi|77689454|ref|ZP_00804635.1| Twin-arginine trans") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[108] self.assertEqual(alignment.title[:50], "gi|77743614|ref|ZP_00812071.1| Twin-arginine trans") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[109] self.assertEqual(alignment.title[:50], "gi|71066141|ref|YP_264868.1| twin-arginine translo") self.assertEqual(alignment.length, 89) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[110] self.assertEqual(alignment.title[:50], "gi|28199457|ref|NP_779771.1| SEC-independent prote") self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[111] self.assertEqual(alignment.title[:50], "gi|15837166|ref|NP_297854.1| hypothetical protein ") self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[112] self.assertEqual(alignment.title[:50], "gi|15074462|emb|CAC46108.1| HYPOTHETICAL TRANSMEMB") self.assertEqual(alignment.length, 68) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[113] self.assertEqual(alignment.title[:50], "gi|27462871|gb|AAO15625.1| Sec-independent protein") self.assertEqual(alignment.length, 63) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[114] self.assertEqual(alignment.title[:50], "gi|35211273|dbj|BAC88652.1| gsl0711 [Gloeobacter v") self.assertEqual(alignment.length, 72) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[115] self.assertEqual(alignment.title[:50], "gi|34482347|emb|CAE09348.1| hypothetical protein [") self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[116] self.assertEqual(alignment.title[:50], "gi|32262257|gb|AAP77305.1| component of Sec-indepe") self.assertEqual(alignment.length, 82) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[117] self.assertEqual(alignment.title[:50], "gi|76261408|ref|ZP_00769019.1| Twin-arginine trans") self.assertEqual(alignment.length, 62) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[118] self.assertEqual(alignment.title[:50], "gi|69933726|ref|ZP_00628928.1| sec-independent tra") self.assertEqual(alignment.length, 159) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[119] self.assertEqual(alignment.title[:50], "gi|15605662|ref|NP_213037.1| hypothetical protein ") self.assertEqual(alignment.length, 59) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[120] self.assertEqual(alignment.title[:50], "gi|68538777|ref|ZP_00578553.1| Twin-arginine trans") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[121] self.assertEqual(alignment.title[:50], "gi|68136098|ref|ZP_00544086.1| Twin-arginine trans") self.assertEqual(alignment.length, 130) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[122] self.assertEqual(alignment.title[:50], "gi|20259265|gb|AAM14368.1| putative Tha4 protein [") self.assertEqual(alignment.length, 147) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[123] self.assertEqual(alignment.title[:50], "gi|75910646|ref|YP_324942.1| Twin-arginine translo") self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[124] self.assertEqual(alignment.title[:50], "gi|39982657|gb|AAR34117.1| twin-arginine transloca") self.assertEqual(alignment.length, 57) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[125] self.assertEqual(alignment.title[:50], "gi|33635687|emb|CAE22011.1| mttA/Hcf106 family [Pr") self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[126] self.assertEqual(alignment.title[:50], "gi|76791934|ref|ZP_00774438.1| Twin-arginine trans") self.assertEqual(alignment.length, 68) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[127] self.assertEqual(alignment.title[:50], "gi|23129516|ref|ZP_00111343.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 91) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[128] self.assertEqual(alignment.title[:50], "gi|48764199|ref|ZP_00268751.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 96) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[129] self.assertEqual(alignment.title[:50], "gi|15677995|ref|NP_273645.1| hypothetical protein ") self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[130] self.assertEqual(alignment.title[:50], "gi|50917153|ref|XP_468973.1| putative sec-independ") self.assertEqual(alignment.length, 170) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[131] self.assertEqual(alignment.title[:50], "gi|16329622|ref|NP_440350.1| hypothetical protein ") self.assertEqual(alignment.length, 126) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[132] self.assertEqual(alignment.title[:50], "gi|71083667|ref|YP_266387.1| Twin-arginine translo") self.assertEqual(alignment.length, 66) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[133] self.assertEqual(alignment.title[:50], "gi|17130190|dbj|BAB72802.1| asl0845 [Nostoc sp. PC") self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[134] self.assertEqual(alignment.title[:50], "gi|68246031|gb|EAN28138.1| Twin-arginine transloca") self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[135] self.assertEqual(alignment.title[:50], "gi|15604583|ref|NP_221101.1| hypothetical protein ") self.assertEqual(alignment.length, 54) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[136] self.assertEqual(alignment.title[:50], "gi|77685166|ref|ZP_00800574.1| Twin-arginine trans") self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[137] self.assertEqual(alignment.title[:50], "gi|39985226|gb|AAR36581.1| twin-arginine transloca") self.assertEqual(alignment.length, 78) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[138] self.assertEqual(alignment.title[:50], "gi|1825636|gb|AAB42258.1| Hypothetical protein ZK3") self.assertEqual(alignment.length, 312) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[139] self.assertEqual(alignment.title[:50], "gi|65321915|ref|ZP_00394874.1| COG5386: Cell surfa") self.assertEqual(alignment.length, 237) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[140] self.assertEqual(alignment.title[:50], "gi|30022625|ref|NP_834256.1| Cell surface protein ") self.assertEqual(alignment.length, 237) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[141] self.assertEqual(alignment.title[:50], "gi|55623442|ref|XP_517520.1| PREDICTED: similar to") self.assertEqual(alignment.length, 234) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[142] self.assertEqual(alignment.title[:50], "gi|75762866|ref|ZP_00742681.1| Cell surface protei") self.assertEqual(alignment.length, 237) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[143] self.assertEqual(alignment.title[:50], "gi|22945598|gb|AAN10511.1| CG18497-PC, isoform C [") self.assertEqual(alignment.length, 5476) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[144] self.assertEqual(alignment.title[:50], "gi|10727420|gb|AAF51534.2| CG18497-PB, isoform B [") self.assertEqual(alignment.length, 5533) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[145] self.assertEqual(alignment.title[:50], "gi|10727421|gb|AAF51535.2| CG18497-PA, isoform A [") self.assertEqual(alignment.length, 5560) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[146] self.assertEqual(alignment.title[:50], "gi|71481981|ref|ZP_00661682.1| Twin-arginine trans") self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[147] self.assertEqual(alignment.title[:50], "gi|71150623|ref|ZP_00649545.1| Twin-arginine trans") self.assertEqual(alignment.length, 81) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[148] self.assertEqual(alignment.title[:50], "gi|20151563|gb|AAM11141.1| LD15253p [Drosophila me") self.assertEqual(alignment.length, 1521) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[149] self.assertEqual(alignment.title[:50], "gi|6979936|gb|AAF34661.1| split ends long isoform ") self.assertEqual(alignment.length, 5554) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[150] self.assertEqual(alignment.title[:50], "gi|6467825|gb|AAF13218.1| Spen RNP motif protein l") self.assertEqual(alignment.length, 5533) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[151] self.assertEqual(alignment.title[:50], "gi|61102013|ref|ZP_00377467.1| hypothetical protei") self.assertEqual(alignment.length, 80) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[152] self.assertEqual(alignment.title[:50], "gi|68056232|ref|ZP_00540361.1| Twin-arginine trans") self.assertEqual(alignment.length, 68) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[153] self.assertEqual(alignment.title[:50], "gi|68190120|gb|EAN04781.1| Twin-arginine transloca") self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[154] self.assertEqual(alignment.title[:50], "gi|15605663|ref|NP_213038.1| hypothetical protein ") self.assertEqual(alignment.length, 77) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[155] self.assertEqual(alignment.title[:50], "gi|60493413|emb|CAH08199.1| aerotolerance-related ") self.assertEqual(alignment.length, 238) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[156] self.assertEqual(alignment.title[:50], "gi|50877510|emb|CAG37350.1| related to Sec-indepen") self.assertEqual(alignment.length, 84) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[157] self.assertEqual(alignment.title[:50], "gi|42739647|gb|AAS43573.1| conserved domain protei") self.assertEqual(alignment.length, 236) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[158] self.assertEqual(alignment.title[:50], "gi|53713708|ref|YP_099700.1| conserved hypothetica") self.assertEqual(alignment.length, 238) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[159] self.assertEqual(alignment.title[:50], "gi|33860901|ref|NP_892462.1| mttA/Hcf106 family [P") self.assertEqual(alignment.length, 96) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[160] self.assertEqual(alignment.title[:50], "gi|48851224|ref|ZP_00305466.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 83) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[161] self.assertEqual(alignment.title[:50], "gi|67938449|ref|ZP_00530974.1| Twin-arginine trans") self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[162] self.assertEqual(alignment.title[:50], "gi|45657833|ref|YP_001919.1| sec-independent prote") self.assertEqual(alignment.length, 90) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[163] self.assertEqual(alignment.title[:50], "gi|57238048|ref|YP_179297.1| twin-arginine translo") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[164] self.assertEqual(alignment.title[:50], "gi|56962648|ref|YP_174374.1| sec-independent prote") self.assertEqual(alignment.length, 63) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[165] self.assertEqual(alignment.title[:50], "gi|33239734|ref|NP_874676.1| Sec-independent prote") self.assertEqual(alignment.length, 84) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[166] self.assertEqual(alignment.title[:50], "gi|21674434|ref|NP_662499.1| Sec-independent prote") self.assertEqual(alignment.length, 67) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[167] self.assertEqual(alignment.title[:50], "gi|39968009|ref|XP_365395.1| hypothetical protein ") self.assertEqual(alignment.length, 823) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[168] self.assertEqual(alignment.title[:50], "gi|4877986|gb|AAD31523.1| THA9 [Zea mays]") self.assertEqual(alignment.length, 169) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[169] self.assertEqual(alignment.title[:50], "gi|67934419|ref|ZP_00527476.1| Twin-arginine trans") self.assertEqual(alignment.length, 56) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[170] self.assertEqual(alignment.title[:50], "gi|42523658|ref|NP_969038.1| twin-argine protein t") self.assertEqual(alignment.length, 79) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[171] self.assertEqual(alignment.title[:50], "gi|71546080|ref|ZP_00666945.1| Twin-arginine trans") self.assertEqual(alignment.length, 73) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[172] self.assertEqual(alignment.title[:50], "gi|68002197|ref|ZP_00534828.1| Twin-arginine trans") self.assertEqual(alignment.length, 60) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[173] self.assertEqual(alignment.title[:50], "gi|67481641|ref|XP_656170.1| hypothetical protein ") self.assertEqual(alignment.length, 434) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[174] self.assertEqual(alignment.title[:50], "gi|50935447|ref|XP_477251.1| putative Calreticulin") self.assertEqual(alignment.length, 424) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[175] self.assertEqual(alignment.title[:50], "gi|50978634|ref|NP_001003013.1| acidic (leucine-ri") self.assertEqual(alignment.length, 249) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[176] self.assertEqual(alignment.title[:50], "gi|70936814|ref|XP_739300.1| 40S ribosomal subunit") self.assertEqual(alignment.length, 184) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[177] self.assertEqual(alignment.title[:50], "gi|68075857|ref|XP_679848.1| hypothetical protein ") self.assertEqual(alignment.length, 340) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[178] self.assertEqual(alignment.title[:50], "gi|39594005|emb|CAE70115.1| Hypothetical protein C") self.assertEqual(alignment.length, 192) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[179] self.assertEqual(alignment.title[:50], "gi|66809957|ref|XP_638702.1| hypothetical protein ") self.assertEqual(alignment.length, 721) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[180] self.assertEqual(alignment.title[:50], "gi|68550463|ref|ZP_00589911.1| Twin-arginine trans") self.assertEqual(alignment.length, 69) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[181] self.assertEqual(alignment.title[:50], "gi|51473916|ref|YP_067673.1| TatA/E-like Sec-indep") self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[182] self.assertEqual(alignment.title[:50], "gi|61857708|ref|XP_612559.1| PREDICTED: similar to") self.assertEqual(alignment.length, 236) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[183] self.assertEqual(alignment.title[:50], "gi|39982651|gb|AAR34111.1| twin-arginine transloca") self.assertEqual(alignment.length, 59) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[184] self.assertEqual(alignment.title[:50], "gi|50877509|emb|CAG37349.1| related to Sec-indepen") self.assertEqual(alignment.length, 66) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[185] self.assertEqual(alignment.title[:50], "gi|52699323|ref|ZP_00340731.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[186] self.assertEqual(alignment.title[:50], "gi|62426215|ref|ZP_00381343.1| COG1826: Sec-indepe") self.assertEqual(alignment.length, 93) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[187] self.assertEqual(alignment.title[:50], "gi|11131838|sp|Q9SLY8|CRTC_ORYSA Calreticulin prec") self.assertEqual(alignment.length, 424) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[188] self.assertEqual(alignment.title[:50], "gi|56543690|gb|AAV89844.1| Sec-independent protein") self.assertEqual(alignment.length, 87) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[189] self.assertEqual(alignment.title[:50], "gi|67923730|ref|ZP_00517196.1| Twin-arginine trans") self.assertEqual(alignment.length, 95) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[190] self.assertEqual(alignment.title[:50], "gi|67462585|ref|XP_647954.1| hypothetical protein ") self.assertEqual(alignment.length, 140) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[191] self.assertEqual(alignment.title[:50], "gi|51970620|dbj|BAD44002.1| unknown protein [Arabi") self.assertEqual(alignment.length, 784) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[192] self.assertEqual(alignment.title[:50], "gi|34581241|ref|ZP_00142721.1| hypothetical protei") self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[193] self.assertEqual(alignment.title[:50], "gi|4877984|gb|AAD31522.1| THA4 [Zea mays]") self.assertEqual(alignment.length, 170) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[194] self.assertEqual(alignment.title[:50], "gi|9757886|dbj|BAB08393.1| unnamed protein product") self.assertEqual(alignment.length, 707) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[195] self.assertEqual(alignment.title[:50], "gi|32422107|ref|XP_331497.1| predicted protein [Ne") self.assertEqual(alignment.length, 216) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[196] self.assertEqual(alignment.title[:50], "gi|68552035|ref|ZP_00591428.1| Twin-arginine trans") self.assertEqual(alignment.length, 70) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[197] self.assertEqual(alignment.title[:50], "gi|68177649|ref|ZP_00550794.1| Twin-arginine trans") self.assertEqual(alignment.length, 58) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[198] self.assertEqual(alignment.title[:50], "gi|67934756|ref|ZP_00527782.1| Twin-arginine trans") self.assertEqual(alignment.length, 65) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[199] self.assertEqual(alignment.title[:50], "gi|42550455|gb|EAA73298.1| hypothetical protein FG") self.assertEqual(alignment.length, 297) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[200] self.assertEqual(alignment.title[:50], "gi|15893083|ref|NP_360797.1| hypothetical protein ") self.assertEqual(alignment.length, 53) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[201] self.assertEqual(alignment.title[:50], "gi|57233621|ref|YP_182297.1| twin-arginine translo") self.assertEqual(alignment.length, 65) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[202] self.assertEqual(alignment.title[:50], "gi|75908036|ref|YP_322332.1| Twin-arginine translo") self.assertEqual(alignment.length, 56) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[203] self.assertEqual(alignment.title[:50], "gi|72383453|ref|YP_292808.1| Twin-arginine translo") self.assertEqual(alignment.length, 71) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[204] self.assertEqual(alignment.title[:50], "gi|1666185|emb|CAB04766.1| ORF13(1) [Rhodococcus e") self.assertEqual(alignment.length, 98) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[205] self.assertEqual(alignment.title[:50], "gi|72138252|ref|XP_800288.1| PREDICTED: hypothetic") self.assertEqual(alignment.length, 946) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[206] self.assertEqual(alignment.title[:50], "gi|67923190|ref|ZP_00516678.1| Twin-arginine trans") self.assertEqual(alignment.length, 50) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[207] self.assertEqual(alignment.title[:50], "gi|3329623|gb|AAC26930.1| Hypothetical protein F36") self.assertEqual(alignment.length, 335) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[208] self.assertEqual(alignment.title[:50], "gi|39597929|emb|CAE68621.1| Hypothetical protein C") self.assertEqual(alignment.length, 2691) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[209] self.assertEqual(alignment.title[:50], "gi|68182025|ref|ZP_00555006.1| hypothetical protei") self.assertEqual(alignment.length, 438) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[210] self.assertEqual(alignment.title[:50], "gi|21204492|dbj|BAB95189.1| ebh [Staphylococcus au") self.assertEqual(alignment.length, 9904) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) alignment = alignments[211] self.assertEqual(alignment.title[:50], "gi|39593039|emb|CAE64508.1| Hypothetical protein C") self.assertEqual(alignment.length, 960) self.assertEqual(len(alignment.hsps), 1) self.assertTrue(alignment.hsps[0].expect > E_VALUE_THRESH) self.assertRaises(StopIteration, records.next) record = NCBIXML.read(open(datafile)) def test_xbt002(self): "Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xbt002)" filename = 'xbt002.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() alignments = record.alignments self.assertEqual(record.query_id, "gi|1348916|gb|G26684.1|G26684") self.assertEqual(len(alignments), 2) self.assertEqual(sum([len(a.hsps) for a in alignments]), 2) self.assertEqual(alignments[0].title[:50], "gi|9950606|gb|AE004854.1| Pseudomonas aeruginosa P") self.assertEqual(alignments[0].length, 11884) self.assertEqual(len(alignments[0].hsps), 1) self.assertTrue(alignments[0].hsps[0].expect > E_VALUE_THRESH) self.assertEqual(alignments[1].title[:50], "gi|15073988|emb|AL591786.1|SME591786 Sinorhizobium") self.assertEqual(alignments[1].length, 299350) self.assertEqual(len(alignments[1].hsps), 1) self.assertTrue(alignments[1].hsps[0].expect > E_VALUE_THRESH) self.assertRaises(StopIteration, records.next) record = NCBIXML.read(open(datafile)) def test_xbt003(self): "Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xbt003)" filename = 'xbt003.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() alignments = record.alignments self.assertEqual(record.query_id, "gi|1347369|gb|G25137.1|G25137") self.assertEqual(len(alignments), 78) self.assertEqual(sum([len(a.hsps) for a in alignments]), 84) self.assertRaises(StopIteration, records.next) record = NCBIXML.read(open(datafile)) def test_xbt004(self): "Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xbt004)" filename = 'xbt004.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() alignments = record.alignments self.assertEqual(record.query_id, "gi|729325|sp|P39483|DHG2_BACME") self.assertEqual(len(alignments), 100) self.assertEqual(sum([len(a.hsps) for a in alignments]), 127) self.assertRaises(StopIteration, records.next) record = NCBIXML.read(open(datafile)) def test_xbt005(self): "Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xbt005)" filename = 'xbt005.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() alignments = record.alignments self.assertEqual(record.query_id, "gi|1348853|gb|G26621.1|G26621") self.assertEqual(len(alignments), 10) self.assertEqual(sum([len(a.hsps) for a in alignments]), 102) self.assertRaises(StopIteration, records.next) record = NCBIXML.read(open(datafile)) def test_xbt006(self): "Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xbt006)" # NOTE - no date in version field, downloaded 2008/05/08 filename = 'xbt006.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() alignments = record.alignments self.assertEqual(record.query_id, "31493") self.assertEqual(len(alignments), 10) self.assertEqual(sum([len(a.hsps) for a in alignments]), 14) self.assertEqual(alignments[0].title[:50], "gi|151942244|gb|EDN60600.1| cytosolic iron-sulfur ") self.assertEqual(alignments[0].length, 330) self.assertEqual(len(alignments[0].hsps), 1) self.assertTrue(alignments[0].hsps[0].expect > E_VALUE_THRESH) self.assertEqual(alignments[1].title[:50], "gi|476059|emb|CAA55606.1| YBR0832 [Saccharomyces c") self.assertEqual(alignments[1].length, 535) self.assertEqual(len(alignments[1].hsps), 1) self.assertTrue(alignments[1].hsps[0].expect > E_VALUE_THRESH) self.assertEqual(alignments[2].title[:50], "gi|6320473|ref|NP_010553.1| Essential protein invo") self.assertEqual(alignments[2].length, 330) self.assertEqual(len(alignments[2].hsps), 1) self.assertTrue(alignments[2].hsps[0].expect > E_VALUE_THRESH) self.assertEqual(alignments[3].title[:50], "gi|61679798|pdb|1R5M|A Chain A, Crystal Structure ") self.assertEqual(alignments[3].length, 425) self.assertEqual(len(alignments[3].hsps), 1) self.assertTrue(alignments[3].hsps[0].expect > E_VALUE_THRESH) self.assertEqual(alignments[4].title[:50], "gi|6319579|ref|NP_009661.1| WD40 repeat-containing") self.assertEqual(alignments[4].length, 535) self.assertEqual(len(alignments[4].hsps), 1) self.assertTrue(alignments[4].hsps[0].expect > E_VALUE_THRESH) self.assertEqual(alignments[5].title[:50], "gi|151946495|gb|EDN64717.1| Sir4p-interacting fact") self.assertEqual(alignments[5].length, 535) self.assertEqual(len(alignments[5].hsps), 1) self.assertTrue(alignments[5].hsps[0].expect > E_VALUE_THRESH) self.assertEqual(alignments[6].title[:50], "gi|151943708|gb|EDN62018.1| nuclear pore complex s") self.assertEqual(alignments[6].length, 349) self.assertEqual(len(alignments[6].hsps), 2) self.assertTrue(alignments[6].hsps[0].expect > E_VALUE_THRESH) self.assertTrue(alignments[6].hsps[1].expect > E_VALUE_THRESH) self.assertEqual(alignments[7].title[:50], "gi|151567866|pdb|2PM7|B Chain B, Crystal Structure") self.assertEqual(alignments[7].length, 297) self.assertEqual(len(alignments[7].hsps), 2) self.assertTrue(alignments[7].hsps[0].expect > E_VALUE_THRESH) self.assertTrue(alignments[7].hsps[1].expect > E_VALUE_THRESH) self.assertEqual(alignments[8].title[:50], "gi|6321338|ref|NP_011415.1| Nuclear pore protein t") self.assertEqual(alignments[8].length, 349) self.assertEqual(len(alignments[8].hsps), 2) self.assertTrue(alignments[8].hsps[0].expect > E_VALUE_THRESH) self.assertTrue(alignments[8].hsps[1].expect > E_VALUE_THRESH) self.assertEqual(alignments[9].title[:50], "gi|151567870|pdb|2PM9|B Chain B, Crystal Structure") self.assertEqual(alignments[9].length, 297) self.assertEqual(len(alignments[9].hsps), 2) self.assertTrue(alignments[9].hsps[0].expect > E_VALUE_THRESH) self.assertTrue(alignments[9].hsps[1].expect > E_VALUE_THRESH) self.assertRaises(StopIteration, records.next) record = NCBIXML.read(open(datafile)) def test_xbt007(self): "Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xbt007)" filename = 'xbt007.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() self.assertEqual(record.query_id, "gi|585505|sp|Q08386|MOPB_RHOCA") alignments = record.alignments self.assertEqual(len(record.alignments), 0) record = records.next() self.assertEqual(record.query_id, "gi|129628|sp|P07175.1|PARA_AGRTU") self.assertEqual(len(record.alignments), 0) self.assertRaises(StopIteration, records.next) def test_xbt008(self): "Parsing BLASTP 2.2.18, Fake query (xbt008)" filename = 'xbt008.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() self.assertEqual(record.query_id, "lcl|1_0") alignments = record.alignments self.assertEqual(len(alignments), 0) self.assertRaises(StopIteration, records.next) record = NCBIXML.read(open(datafile)) def test_xbt009(self): "Parsing BLASTX 2.2.22+, multiple queries against NR (xbt009)" #See also plain text file bt081.txt (matching output from blastx tool) filename = 'xbt009.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, '2.2.22+') self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|4104054|gb|AH007193.1|SEG_CVIGS Centaurea vallesiaca 18S ribosomal RNA gene, partial sequence") self.assertEqual(record.query_letters, 1002) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) #self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) #NCBI bug! self.assertEqual(len(record.descriptions), 1) self.assertEqual(len(record.alignments), 1) self.assertEqual(len(record.alignments[0].hsps), 1) record = records.next() self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, '2.2.22+') self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|4218935|gb|AF074388.1|AF074388 Sambucus nigra hevein-like protein HLPf gene, partial cds") self.assertEqual(record.query_letters, 2050) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) #self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) #NCBI bug! # I used -num_descriptions 10 and -num_alignments 1 self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 2) self.assertEqual(len(record.alignments[1].hsps), 2) self.assertEqual(len(record.alignments[9].hsps), 2) record = records.next() self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, '2.2.22+') self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|5690369|gb|AF158246.1|AF158246 Cricetulus griseus glucose phosphate isomerase (GPI) gene, partial intron sequence") self.assertEqual(record.query_letters, 550) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) #self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) #NCBI bug! self.assertEqual(len(record.descriptions), 0) self.assertEqual(len(record.alignments), 0) record = records.next() self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, '2.2.22+') self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|5049839|gb|AI730987.1|AI730987 BNLGHi8354 Six-day Cotton fiber Gossypium hirsutum cDNA 5' similar to TUBULIN BETA-1 CHAIN gi|486734|pir|S35142 tubulin beta chain - white lupine gi|402636 (X70184) Beta tubulin 1 [Lupinus albus], mRNA sequence") self.assertEqual(record.query_letters, 655) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) #self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) #NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 1) self.assertEqual(len(record.alignments[9].hsps), 1) record = records.next() self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, '2.2.22+') self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|5052071|gb|AF067555.1|AF067555 Phlox stansburyi internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence") self.assertEqual(record.query_letters, 623) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) #self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) #NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 2) self.assertEqual(len(record.alignments[9].hsps), 1) record = records.next() self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, '2.2.22+') self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|3176602|gb|U78617.1|LOU78617 Lathyrus odoratus phytochrome A (PHYA) gene, partial cds") self.assertEqual(record.query_letters, 309) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) #self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) #NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 1) self.assertEqual(len(record.alignments[9].hsps), 1) record = records.next() self.assertEqual(record.application, "BLASTX") self.assertEqual(record.version, '2.2.22+') self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|5817701|gb|AF142731.1|AF142731 Wisteria frutescens maturase-like protein (matK) gene, complete cds; chloroplast gene for chloroplast product") self.assertEqual(record.query_letters, 2551) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) #self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) #NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 1) self.assertEqual(len(record.alignments[9].hsps), 1) self.assertRaises(StopIteration, records.next) def test_xbt010(self): "Parsing BLASTP 2.2.22+, multiple queries against NR (xbt010)" #This is from blastp NOT blastall filename = 'xbt010.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, '2.2.22+') self.assertEqual(record.date, "") self.assertEqual(record.query, "gi|3298468|dbj|BAA31520.1| SAMIPF") self.assertEqual(record.query_letters, 107) self.assertEqual(record.database, "nr") self.assertEqual(record.num_sequences_in_database, 8994603) self.assertEqual(record.database_sequences, 8994603) #self.assertEqual(record.database_length, 3078807967) self.assertEqual(record.database_length, -1216159329) #NCBI bug! self.assertEqual(len(record.descriptions), 10) self.assertEqual(len(record.alignments), 10) self.assertEqual(len(record.alignments[0].hsps), 1) record = records.next() self.assertEqual(record.query, "gi|2781234|pdb|1JLY|B Chain B, Crystal Structure Of Amaranthus Caudatus Agglutinin") self.assertEqual(record.query_letters, 304) record = records.next() self.assertEqual(record.query, "gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING finger protein") self.assertEqual(record.query_letters, 600) record = records.next() self.assertEqual(record.query, "gi|671626|emb|CAA85685.1| rubisco large subunit") self.assertEqual(record.query_letters, 473) self.assertRaises(StopIteration, records.next) def test_xbt011(self): "Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xbt011)" #This is from old pgpblast command line tool, NOT new psiblast #NOTE - The parser currently returns three BLAST record objects. #The old text parser would return a single PSI BLAST record object with three rounds. #This may change... although it may require a PSI BLAST specific XML parser. filename = 'xbt011.xml' datafile = os.path.join("Blast", filename) records = NCBIXML.parse(open(datafile)) record = records.next() self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, '2.2.18') self.assertEqual(record.date, "Mar-02-2008") self.assertEqual(record.query, "tr|Q3V4Q3|Q3V4Q3_9VIRU") self.assertEqual(record.query_letters, 131) self.assertEqual(record.database, "/opt/BlastDBs/nr") self.assertEqual(record.num_sequences_in_database, 2563094) self.assertEqual(record.database_sequences, 2563094) self.assertEqual(record.database_length, 864488805) self.assertEqual(len(record.descriptions), 11) self.assertEqual(len(record.alignments), 11) self.assertEqual(len(record.alignments[0].hsps), 1) hsp = record.alignments[0].hsps[0] self.assertEqual(hsp.align_length, 131) self.assertEqual(hsp.identities, 131) self.assertEqual(hsp.positives, 131) self.assertEqual(hsp.query, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.sbjct, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.match, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.score, 680) self.assertEqual(hsp.expect, 4.72196e-70) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 131) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 131) self.assertEqual(len(record.alignments[1].hsps), 1) hsp = record.alignments[1].hsps[0] self.assertEqual(hsp.align_length, 77) self.assertEqual(hsp.identities, 36) self.assertEqual(hsp.positives, 49) self.assertEqual(hsp.query, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQ") self.assertEqual(hsp.sbjct, "MAREEPYKGDYVGGVAKILQGYFANYYGFPNVSLRLAGEEANLSKTGHANAKAIVHEMIKVIKEASKPLR-RGKGFK") self.assertEqual(hsp.match, "MA+ EP KGDY GG KIL + G+P V+L+LAGEEAN + G K +H ++K+I +A KP R +G GF+") self.assertEqual(hsp.score, 181) self.assertEqual(hsp.expect, 3.03476e-12) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 77) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 76) record = records.next() self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, '2.2.18') self.assertEqual(record.date, "Mar-02-2008") self.assertEqual(record.query, "tr|Q3V4Q3|Q3V4Q3_9VIRU") self.assertEqual(record.query_letters, 131) self.assertEqual(record.database, "/opt/BlastDBs/nr") self.assertEqual(record.num_sequences_in_database, 2563094) self.assertEqual(record.database_sequences, 2563094) self.assertEqual(record.database_length, 864488805) self.assertEqual(len(record.descriptions), 19) self.assertEqual(len(record.alignments), 19) self.assertEqual(len(record.alignments[0].hsps), 1) hsp = record.alignments[0].hsps[0] self.assertEqual(hsp.align_length, 131) self.assertEqual(hsp.identities, 131) self.assertEqual(hsp.positives, 131) self.assertEqual(hsp.query, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.sbjct, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.match, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.score, 590) self.assertEqual(hsp.expect, 1.28615e-59) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 131) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 131) record = records.next() self.assertEqual(record.application, "BLASTP") self.assertEqual(record.version, '2.2.18') self.assertEqual(record.date, "Mar-02-2008") self.assertEqual(record.query, "tr|Q3V4Q3|Q3V4Q3_9VIRU") self.assertEqual(record.query_letters, 131) self.assertEqual(record.database, "/opt/BlastDBs/nr") self.assertEqual(record.num_sequences_in_database, 2563094) self.assertEqual(record.database_sequences, 2563094) self.assertEqual(record.database_length, 864488805) self.assertEqual(len(record.descriptions), 9) self.assertEqual(len(record.alignments), 9) self.assertEqual(len(record.alignments[0].hsps), 1) hsp = record.alignments[0].hsps[0] self.assertEqual(hsp.align_length, 131) self.assertEqual(hsp.identities, 131) self.assertEqual(hsp.positives, 131) self.assertEqual(hsp.query, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.sbjct, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.match, "MAKYEPKKGDYAGGAVKILDMFENGQLGYPEVTLKLAGEEANARRAGDERTKEAIHAIVKMISDAMKPYRNKGSGFQSQPIPGEVIAQVTSNPEYQQAKAFLASPATQVRNIEREEVLSKGAKKLAQAMAS") self.assertEqual(hsp.score, 535) self.assertEqual(hsp.expect, 3.43623e-53) self.assertEqual(hsp.query_start, 1) self.assertEqual(hsp.query_end, 131) self.assertEqual(hsp.sbjct_start, 1) self.assertEqual(hsp.sbjct_end, 131) #TODO - Can we detect the convergence status: #CONVERGED self.assertRaises(StopIteration, records.next) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity = 2) unittest.main(testRunner=runner)