Mercurial > repos > yufei-luo > s_mart
comparison commons/tools/tests/Test_AlignTEOnGenomeAccordingToAnnotation.py @ 18:94ab73e8a190
Uploaded
| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 17:b0e8584489e6 | 18:94ab73e8a190 |
|---|---|
| 1 from commons.core.seq.Bioseq import Bioseq | |
| 2 from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB | |
| 3 from commons.core.sql.DbFactory import DbFactory | |
| 4 from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator | |
| 5 from commons.core.sql.TablePathAdaptator import TablePathAdaptator | |
| 6 from commons.core.coord.Path import Path | |
| 7 import os | |
| 8 import unittest | |
| 9 from commons.tools.AlignTEOnGenomeAccordingToAnnotation import AlignTEOnGenomeAccordingToAnnotation | |
| 10 | |
| 11 class Test_AlignTEOnGenomeAccordingToAnnotation(unittest.TestCase): | |
| 12 | |
| 13 def test_alignBioseqWithNWalign(self): | |
| 14 iBioseq1 = Bioseq("dmel_chr4", "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAGTAGAAGAAA") | |
| 15 iBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTTCTTCTACCTATTACATACTTTTCAACAAATCTAGCATACCCTTTTACTCTACGAGTA") | |
| 16 iAlignedBioseq1 = Bioseq("dmel_chr4 Score=58 Identity=0.7", "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTT-TAGA-AGTACGTTACTAGTAGAAGAAA----------------------------") | |
| 17 iAlignedBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat Score=58 Identity=0.7", "----------------------------TTTCTTCTACCTATTACAT-ACTTTTC-AACAAATCTAGCATACCCTTTTACTCTACGAGTA") | |
| 18 expiAlignedBioseqDB = AlignedBioseqDB() | |
| 19 expiAlignedBioseqDB.add(iAlignedBioseq1) | |
| 20 expiAlignedBioseqDB.add(iAlignedBioseq2) | |
| 21 | |
| 22 iATEOGATA = AlignTEOnGenomeAccordingToAnnotation() | |
| 23 obsiAlignedBioseqDB = iATEOGATA.alignBioseqWithNWalign(iBioseq1, iBioseq2) | |
| 24 | |
| 25 self.assertEquals(expiAlignedBioseqDB, obsiAlignedBioseqDB) | |
| 26 | |
| 27 def test_alignSeqAccordingToPathAndBuildAlignedSeqTable_one_path(self): | |
| 28 iBioseq1 = Bioseq("dmel_chr4", "TTTCTTCTACTAGTAACGTACTTCTAAACAAATCTCTCATACCCTTTTCCTCTACGATTA") | |
| 29 iBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGATCAGTGTTTGTTGGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGATC") | |
| 30 iPath = Path() | |
| 31 iPath.setFromTuple((1, "dmel_chr4", 1, 60, "DmelChr4-B-R1-Map4_NoCat", 315, 256, 0, 249, 81.67)) | |
| 32 | |
| 33 seqTable1 = "seqTable1_seq" | |
| 34 seqTable2 = "seqTable2_seq" | |
| 35 pathTable = "pathTable_path" | |
| 36 | |
| 37 iDb = DbFactory.createInstance() | |
| 38 iDb.createTable(seqTable1, "seq", overwrite = True) | |
| 39 iDb.createTable(seqTable2, "seq", overwrite = True) | |
| 40 iDb.createTable(pathTable, "path", overwrite = True) | |
| 41 | |
| 42 iTSA1 = TableSeqAdaptator(iDb, seqTable1) | |
| 43 iTSA2 = TableSeqAdaptator(iDb, seqTable2) | |
| 44 iTPA = TablePathAdaptator(iDb, pathTable) | |
| 45 iTSA1.insert(iBioseq1) | |
| 46 iTSA2.insert(iBioseq2) | |
| 47 iTPA.insert(iPath) | |
| 48 | |
| 49 expTTuples = ((1, "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAG-TAGAAGAAA", "TACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGT-AATAGGTAGAAGAAA", 406, 86.440700000000004),) | |
| 50 | |
| 51 iATEOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTable, seqTable1, seqTable2) | |
| 52 iATEOGATA.setMergeSamePathId(True) | |
| 53 iATEOGATA.setDbInstance(iDb) | |
| 54 iATEOGATA.alignSeqAccordingToPathAndBuildAlignedSeqTable() | |
| 55 | |
| 56 #TODO: "select * from ..." + execute + fetchall => create method in TableAdaptator | |
| 57 sqlCmd = "SELECT * FROM %s_align" % pathTable | |
| 58 iDb.execute(sqlCmd) | |
| 59 obsTTuples = iDb.fetchall() | |
| 60 | |
| 61 iDb.dropTable(seqTable1) | |
| 62 iDb.dropTable(seqTable2) | |
| 63 iDb.dropTable(pathTable) | |
| 64 iDb.dropTable("%s_align" % pathTable) | |
| 65 iDb.close() | |
| 66 | |
| 67 self.assertEquals(expTTuples, obsTTuples) | |
| 68 | |
| 69 def test_alignSeqAccordingToPathAndBuildAlignedSeqTable_n_paths(self): | |
| 70 queryTableName = "query_seq" | |
| 71 subjectTableName = "subject_seq" | |
| 72 pathTableName = "table_path" | |
| 73 | |
| 74 iDb = DbFactory.createInstance() | |
| 75 queryFileName = "dummyDmelChr4.fa" | |
| 76 self._writeDummyDmelChr4(queryFileName) | |
| 77 iDb.createTable(queryTableName, "seq", queryFileName, True) | |
| 78 os.remove(queryFileName) | |
| 79 iDb.createTable(subjectTableName, "seq", overwrite = True) | |
| 80 iDb.createTable(pathTableName, "path", overwrite = True) | |
| 81 | |
| 82 iTSA = TableSeqAdaptator(iDb, subjectTableName) | |
| 83 iTPA = TablePathAdaptator(iDb, pathTableName) | |
| 84 iBioseq1 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGATCAGTGTTTGTTGGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGATC") | |
| 85 iBioseq2 = Bioseq("DmelChr4-B-R4-Map5_NoCat", "CCAAAATTGCCCTCTTTCCGCTCGCTCACGCTGAGAGCATAAGAAATCTAAAAATAGAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGTGTGCGTGTTGTGCTAGAAGACTATTTTCGGGCCGAAATCAATTCTGATCGAAAAAACGAATTTACATTGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAATAAAATAATTTTTAAAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTAAAATTTGTTTGTTAAAATCGCCGATCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATATTTTTTTTGAAACACTTTTAATGTTAAAAATGACTTAATAAATATACTAAATAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAAAATATGATAACTGTTTATTGCAAAAGTCATATCAAAGACACTAGAATTATTCTAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAAAGTCAAAGAACTTCTAAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACAGTTGTCTGCTATCACTTTATGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTCCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCGAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGGTA") | |
| 86 iBioseq3 = Bioseq("DmelChr4-B-G9-Map3_NoCat", "ACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAAAAAAAAATTTTTTTTAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAAACACTTTTAATGTTAATGTTACATCATATTAAGTCAAATGATTTAATAAATATACTAAATAATTAAATATGATAACTGTTTATTGCAAAAGTAATATCAAAGACACTAGAATAATTCTAATGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCCCTCAACAATCATTGGCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGAAAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAACGTCTAAGAACTTCTGAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACATTTGTCTGCTATCACTTTGTGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACAAATGTATGTGTGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTCAGAAGTTCTTAGACGTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTTTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGCCAATGATTGTTGAGGGCTTGTGTCCGCACTTCGTGC") | |
| 87 iTSA.insert(iBioseq1) | |
| 88 iTSA.insert(iBioseq2) | |
| 89 iTSA.insert(iBioseq3) | |
| 90 iPath = Path() | |
| 91 iPath.setFromTuple((1, "dmel_chr4", 1, 60, "DmelChr4-B-R1-Map4_NoCat", 315, 256, 0, 249, 81.67)) | |
| 92 iTPA.insert(iPath) | |
| 93 iPath.setFromTuple((28, "dmel_chr4", 280, 1380, "DmelChr4-B-G9-Map3_NoCat", 3, 1100, 0, 7456, 94.400000))#28 => seems to be a join from "long join" | |
| 94 iTPA.insert(iPath) | |
| 95 iPath.setFromTuple((28, "dmel_chr4", 8971, 9459, "DmelChr4-B-G9-Map3_NoCat", 1102, 1590, 0, 758, 96.707800)) | |
| 96 iTPA.insert(iPath) | |
| 97 iPath.setFromTuple((30, "dmel_chr4", 9815, 9826, "DmelChr4-B-G9-Map3_NoCat", 574, 563, 0, 4, 78.162700))#30 => seems to be a join from "matcher" | |
| 98 iTPA.insert(iPath) | |
| 99 iPath.setFromTuple((30, "dmel_chr4", 9957, 10047, "DmelChr4-B-G9-Map3_NoCat", 429, 337, 0, 33, 78.162700)) | |
| 100 iTPA.insert(iPath) | |
| 101 iPath.setFromTuple((30, "dmel_chr4", 10094, 10127, "DmelChr4-B-G9-Map3_NoCat", 290, 256, 0, 13, 78.162700)) | |
| 102 iTPA.insert(iPath) | |
| 103 | |
| 104 expTTuples = ((1, "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAG-TAGAAGAAA", "TACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGT-AATAGGTAGAAGAAA", 406, 86.440700000000004),\ | |
| 105 (28, "CAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCGGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGAGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTATCAATATGATAAAATAAAAAAATTTTTAAAAATTCGCGCCCTGACTATTATAACTTGAAAGTTTTTTAAATTTGTTTGTTAAAAT-----------TT-------GTT---------------ATGTTTAATTCTAATTTGTCTGACAATCTGACATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAA-CACTTTTAATGTTAATGTTACATCATTTTAAGTCAAATGACTTATTAAATATACTAATTAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAA--AATATGATA---ACTAGAATTATTCCAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTCTTATATTTTTAAATAATAATAACGTTAAGGCAATGCAAA-CAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATACAGATTTAAAGTCTAAGAACTTCTAGGGTGAAGGGCTTTTTTTGTCAAATTTACAATGCATGAGCATTCGTGTGCACACATAAAGTTGTCTGCTATCACTGTATGCGTAGAAAAGAGCTGTTTGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACAATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACCGCTCTTTTCTACGCATACAGTGATAGCAGACAACTTTATGTGCGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCGTAGAAGTTCTTAGACTTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATAATATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGGGTGTGAAAAATGAATAAGGCAATGATTGTTG----CTTGTGTCCGTCCGCACTTCGTGC", "CAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAAAAAAAAATTTTTTTTAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCT------CT--CATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAAACACTTTTAATGTTAATGTTACATCATATTAAGTCAAATGATTTAATAAATATACTAAATAATTAAA-----------------TATGATAACT---GT--TT------ATTGCA-AAAGTAATATCAAAGACACTAGAATAATTCTAATG------CTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCCCTCAACAATCATTGGCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGAAAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAACGTCTAAGAACTTCTGAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACATTTGTCTGCTATCACTTTGTGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACAAATGTATGTGTGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTCAGAAGTTCTTAGACGTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTTTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGCCAATGATTGTTGAGGGCTTGTGTCCG----CACTTCGTGC", 13732, 96.1763),\ | |
| 106 (30, "------------------------------------ACATTTACAT-TTTTTGAATTTGTGGG-------CGTGGCA-GAACGGGCAATAT-GTATGCATA---ATATGTATGCATAATCTCTACCTTCTTGCTTTTATAGTTCCTGAGACCTCGACGTTCATACGGACAGACGAAATATGCGAAA", "ACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGC--TACCGTTTACACATTTATATTTATGTTTAAT-TCTAATTTGTCAATATCAAAGAC-------------------------------------------", 158, 64.835200000000004)) | |
| 107 | |
| 108 iATEOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTableName, queryTableName, subjectTableName) | |
| 109 iATEOGATA.setMergeSamePathId(True) | |
| 110 iATEOGATA.setDbInstance(iDb) | |
| 111 iATEOGATA.alignSeqAccordingToPathAndBuildAlignedSeqTable() | |
| 112 | |
| 113 #TODO: "select * from ..." + execute + fetchall => create method in TableAdaptator | |
| 114 sqlCmd = "SELECT * FROM %s_align" % pathTableName | |
| 115 iDb.execute(sqlCmd) | |
| 116 obsTTuples = iDb.fetchall() | |
| 117 | |
| 118 iDb.dropTable(queryTableName) | |
| 119 iDb.dropTable(subjectTableName) | |
| 120 iDb.dropTable(pathTableName) | |
| 121 iDb.dropTable("%s_align" % pathTableName) | |
| 122 iDb.close() | |
| 123 | |
| 124 self.assertEquals(expTTuples, obsTTuples) | |
| 125 | |
| 126 def _writeDummyDmelChr4(self, fileName): | |
| 127 with open(fileName, "w") as f: | |
| 128 f.write(">dmel_chr4\n") | |
| 129 f.write("TTTCTTCTACTAGTAACGTACTTCTAAACAAATCTCTCATACCCTTTTCCTCTACGATTA\n") | |
| 130 f.write("TGTTGGTATTAATGGTCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAG\n") | |
| 131 f.write("AATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAG\n") | |
| 132 f.write("AAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTAC\n") | |
| 133 f.write("TTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGCAAAGACACTAGAATAACAAG\n") | |
| 134 f.write("ATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAA\n") | |
| 135 f.write("ATTACTCTCTTTCGGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCT\n") | |
| 136 f.write("TGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGAGTGCGTGTTGTGCTAGAA\n") | |
| 137 f.write("GACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTA\n") | |
| 138 f.write("GGGTAGTTTTTGCCAATTTCCTATCAATATGATAAAATAAAAAAATTTTTAAAAATTCGC\n") | |
| 139 f.write("GCCCTGACTATTATAACTTGAAAGTTTTTTAAATTTGTTTGTTAAAATTTGTTATGTTTA\n") | |
| 140 f.write("ATTCTAATTTGTCTGACAATCTGACATCTGACAATTTTTTAAAAGCGAAATATTTTTTTA\n") | |
| 141 f.write("AACACTTTTAATGTTAATGTTACATCATTTTAAGTCAAATGACTTATTAAATATACTAAT\n") | |
| 142 f.write("TAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAA\n") | |
| 143 f.write("AATATGATAACTAGAATTATTCCAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGT\n") | |
| 144 f.write("GCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAAT\n") | |
| 145 f.write("ACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATAT\n") | |
| 146 f.write("GTACATAGATTTGGCTATTTCTCTTATATTTTTAAATAATAATAACGTTAAGGCAATGCA\n") | |
| 147 f.write("AACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATACAGATTTAAAGTCTAAGA\n") | |
| 148 f.write("ACTTCTAGGGTGAAGGGCTTTTTTTGTCAAATTTACAATGCATGAGCATTCGTGTGCACA\n") | |
| 149 f.write("CATAAAGTTGTCTGCTATCACTGTATGCGTAGAAAAGAGCTGTTTGCTGTAGCGCTCTTC\n") | |
| 150 f.write("GCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCC\n") | |
| 151 f.write("AAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTG\n") | |
| 152 f.write("GTAAAATGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAAAAGAAAGCGTTTTCGA\n") | |
| 153 f.write("CCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGC\n") | |
| 154 f.write("CATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCA\n") | |
| 155 f.write("CAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTG\n") | |
| 156 f.write("TCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCA\n") | |
| 157 f.write("TCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGT\n") | |
| 158 f.write("TCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGC\n") | |
| 159 f.write("TTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTA\n") | |
| 160 f.write("TAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTA\n") | |
| 161 f.write("CGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTAT\n") | |
| 162 f.write("TGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATT\n") | |
| 163 f.write("TTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCT\n") | |
| 164 f.write("TTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTA\n") | |
| 165 f.write("TTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTT\n") | |
| 166 f.write("GGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTC\n") | |
| 167 f.write("CTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGT\n") | |
| 168 f.write("TTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTA\n") | |
| 169 f.write("ACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACC\n") | |
| 170 f.write("GTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCA\n") | |
| 171 f.write("TAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAA\n") | |
| 172 f.write("ACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAA\n") | |
| 173 f.write("AAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCA\n") | |
| 174 f.write("TCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATA\n") | |
| 175 f.write("TCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAA\n") | |
| 176 f.write("AATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATA\n") | |
| 177 f.write("ACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCA\n") | |
| 178 f.write("TCGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACT\n") | |
| 179 f.write("CTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATT\n") | |
| 180 f.write("AATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGT\n") | |
| 181 f.write("ATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTAT\n") | |
| 182 f.write("TCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTA\n") | |
| 183 f.write("ATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGAT\n") | |
| 184 f.write("AGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCC\n") | |
| 185 f.write("GTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTA\n") | |
| 186 f.write("TTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGA\n") | |
| 187 f.write("TCGACTCGCATATTGATGCTGATCAAGAATATTTATATTTTACATGATCGGAAACGCTTC\n") | |
| 188 f.write("ATTGCTCTACGAGTAATGGGTACAATAATTTAAAACAAACATATTAAAAGTATAGCAAAA\n") | |
| 189 f.write("CCCTATCTGAAGGACTAAAATTTTATCGCATTTTAAAATTTGTTGCATTAAAATCTTTGA\n") | |
| 190 f.write("TAACCTTTCGTTGAATTAGGTGCTTCGACTTTTTTTACCCTAAGAACAATTTCGATTTGG\n") | |
| 191 f.write("CATACATTGAAAACGTAGAAACTCAACCCTGCATTCATTCATAGAACTTATAAAGAGCTA\n") | |
| 192 f.write("CATCTTCGAAAATAAAAAAAAGGTTTGTTTTTAAGACTTAATGCGTACAATGTCGCTTTC\n") | |
| 193 f.write("GACATTAGGGTATTGCTAGAATTAATATTCGCTTTGTTGTTTACTTTTCCAAACAAACAT\n") | |
| 194 f.write("AATGGGTAAACCAAAAAAATGGGAAACGTCAGTATTAAGTGCTATCGAAAACGTTTAGAA\n") | |
| 195 f.write("TATGGAGAATCTAGTTGTTATTACCAAAACGCATAAATACTAAGCATATACTAAAACAAA\n") | |
| 196 f.write("ATAGAAAAAGATAATGTTTATTTTAGACTCACCTTAGCAAACAGCAACTTATTCGACGGC\n") | |
| 197 f.write("GAATCTTTTCCAAGTCTGTGCTCTGATGTTAAACAAGCGTCCATAAATGTTTGTGCAATG\n") | |
| 198 f.write("ACACTTAAACAGGAATCAACGCTGTATGTTTTATTTACATCAAATATAAAATCCGGATTT\n") | |
| 199 f.write("TTTATAAAATTAACCCAGAATCGAAGGGGCAAACAATTTGACTTCCAAGCGTGCACAATA\n") | |
| 200 f.write("TCAGTATCAGCAATATCATGGCGTCGCGCAGCTTCATCAAGTAAGTCAAAGAGCCATTTA\n") | |
| 201 f.write("ACGGCAGGTGGCAACTCCTCATTAACAGTTAAAATAATTGAGAAAAAATCATCAACAAAT\n") | |
| 202 f.write("TTTTGTATAGTTCCTTTTGTGGCCAGAAGACGCGTAAGGTAAACTTCTGGTATTGTTTTG\n") | |
| 203 f.write("TTCACCCTGTCATTACAATTATTAACGACATGCGATTGAAATGCTGGTGATCCTCCGGAT\n") | |
| 204 f.write("AACACGGAATTTTTAATGTTCATATAATGATCAGGTATATTGGGCTTAACAAGATGGTAA\n") | |
| 205 f.write("ACCCGGGGCTGCTGCAAACCTGATTCGATATCATTATTAATTATAATATGACTTTGCGAA\n") | |
| 206 f.write("TTGTTTATAAAATAAACTGCAAAAAGGCAAAACAATTAATTAAAAAATTTTTAGATATTG\n") | |
| 207 f.write("GGCTTAGTACTTACAATTGTGGTATGGTGCCGAATTTTGGTTTTTACTGTATGGTATATG\n") | |
| 208 f.write("ATAATTATCATTTTGACGTGCAATTAGTGACATTACTGCAGATTCTTTGACTCCATAATG\n") | |
| 209 f.write("AGCTAATGTGTTAAGGCGCTTCCATCCGTTAACGGTTTTGGTTGTCAAGTCTTCATCTTG\n") | |
| 210 f.write("TAATGTAAGATGACCTCCTCGGCCGTGCCTCCATTCTAAGTCTACTTCGTTTACAGATGG\n") | |
| 211 f.write("CCTCATAGAGAAAGGAGTGTTTTTAAAAATTGCGTCGAGGATTTTAAGCTTAACTTGAGA\n") | |
| 212 f.write("AATGGTATCCCAATCGTTAACGCGACATTGGACTTTTTCATCAAGATCATCTTGTAAAAT\n") | |
| 213 f.write("ATGCTATATTACAACAGAATGGGTAACTTGTTCATGCAGAAGACGTTCTTCTGAAAGGGA\n") | |
| 214 f.write("GTAACGGGCATCGTTGGTTATTGCGTCCACTAAACCCTTTTCAATTTGATGCTTTATTGC\n") | |
| 215 f.write("TTTGAAGAGCAAAAATAAATTTGATCCGGCGTACTCTTTCAGGTAATCGTACATACAAAT\n") | |
| 216 f.write("TGCTAGGTAGTTGGTCAACATTTTTTCAACAACGCTTTCAGTACGCCTTAGCATCAGCTG\n") | |
| 217 f.write("AGGATGTTTGCTGGCAAGTGATTTATCTATCAAACGTAATAAAAGGGACTTCAAAATTTC\n") | |
| 218 f.write("CGTGGCATATTCCATCTTGTTCATTAAAACAACCATTATTAATGAGGCAACGTTAACTCG\n") | |
| 219 f.write("GTCTCTAATAGAAAATGATGAACGTTGAGCTTCTAATGTTTCTATGAACATTAATAAAAA\n") | |
| 220 f.write("ATATTTATTGCCAATCAGTTGTTCAAATTGTACCATAGCTGCGTCATAGTTAGTCTGTGG\n") | |
| 221 f.write("GCTACCTTCACGAAATTTTGGAGAATTTAAAATAGGATGATCTGATACACCAGGGAAAAA\n") | |
| 222 f.write("CACCTTCATAATATAGTTGACGTGATCTAAAGTTGGTATGCCTGTGCTCTCCAAATCTGC\n") | |
| 223 f.write("TGTTAGGTCGGTCATGTCCGTTTGGAGCTCAGCGAATGCCTGTTTACACTCAGAACGTAC\n") | |
| 224 f.write("GTTGCTTTCTAATGTAATCATCTGTATCTGAATACGTTTATACTCGCGTTCTGCTTGTGT\n") | |
| 225 f.write("TGATTTCCTTCTGAATATTATAAGTACAATTACAAAAACAACGACCAGAAGTGCTACCGT\n") | |
| 226 f.write("TAATATGCCGACTAACAAGGCATGTGAGAAAACATAGGGTTTATTTAAATCATACTTAAG\n") | |
| 227 f.write("ATATCCTATTACAAAACGAAGATTTCGACCTACTTTAACGACAACAAGAGGTAAATCAGT\n") | |
| 228 f.write("TGATTGATCCACACCATTTTCATCAGTTGGAAGTGGTTGTTGCTCCGGCGGAATGCATAA\n") | |
| 229 f.write("AAGTTGGTTAAGTGCCAGGCTGGTAATATTGCATTGGGAAGTTCCAATAGTTACATTTAC\n") | |
| 230 f.write("ATCGTACTCATCAGCTGCCAAGTTTAATAGCTCGCCTTCTATGACCAAGCTGTCACCCTT\n") | |
| 231 f.write("GTAGAGTTTAACGCCGTCGTTGGGAAATGGCAAATATTTTGGGTCTGCTAAATAGACAAT\n") | |
| 232 f.write("AGTGCTCCTTATGTCATGAAAATATTTATTCAAGTTTCGAACTAGTTGTACATTGTCCAT\n") | |
| 233 f.write("TACAAAACTTAGTTGTAAGTTAAATTGAGTTTCATGAACCTTAACGAATGTGGTGACGTC\n") | |
| 234 f.write("CATATTATTGTTAACAAAATAGTTGGCTGAAGATCCTGCATTTGTGTATAAGCGAAAAGT\n") | |
| 235 f.write("GTCTCCAAAGTCGGCTCGCCGCTTTTTTCTATCATATTCATTTTTATACCTGGTTTCAGT\n") | |
| 236 f.write("TTGAAACGAAGAATTTTGTAAGTGCAATTCAGTATCCATCTTTCTGTTCGTCTTTTTAAA\n") | |
| 237 f.write("AGTCTCAAATTTTTAATTTACCGGAGGAGATGGACATTCCATTTGATTAGAGTTGATCAC\n") | |
| 238 f.write("CACACAAGATGTTTTATTTACTCTTTCATTGTCATAAAACACTTCTAGTTCAGGTTTTTG\n") | |
| 239 f.write("GTTTTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGTTCAGTGTTTGTT\n") | |
| 240 f.write("GGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATT\n") | |
| 241 f.write("TCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAAC\n") | |
| 242 f.write("TTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGT\n") | |
| 243 f.write("TAGTCTTAATAATACCCGTACTTGTAGAGTAAAAGGGTATGCTAGATTTGTAGAAAAGTA\n") | |
| 244 f.write("TGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGG\n") | |
| 245 f.write("ATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAG\n") | |
| 246 f.write("AGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCG\n") | |
| 247 f.write("ATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACT\n") | |
| 248 f.write("TTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAAT\n") | |
| 249 f.write("ATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGG\n") | |
| 250 f.write("GAAACTCAACCATAACATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAA\n") | |
| 251 f.write("GAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTAT\n") | |
| 252 f.write("ATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCA\n") | |
| 253 f.write("ACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAAT\n") | |
| 254 f.write("GGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGT\n") | |
| 255 f.write("TATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTA\n") | |
| 256 f.write("AGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGT\n") | |
| 257 f.write("CAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCC\n") | |
| 258 f.write("TTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAG\n") | |
| 259 f.write("TCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGG\n") | |
| 260 f.write("CTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAG\n") | |
| 261 f.write("ATATAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATAT\n") | |
| 262 f.write("TTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTCTCTTA\n") | |
| 263 f.write("CATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAA\n") | |
| 264 f.write("ATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTAAAAAATCATATTG\n") | |
| 265 f.write("ATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCG\n") | |
| 266 f.write("TGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACA\n") | |
| 267 f.write("AAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGA\n") | |
| 268 f.write("TCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCT\n") | |
| 269 f.write("TCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGT\n") | |
| 270 f.write("GGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCC\n") | |
| 271 f.write("TGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACT\n") | |
| 272 f.write("TATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAAT\n") | |
| 273 f.write("ATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATT\n") | |
| 274 f.write("TGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATA\n") | |
| 275 f.write("GGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACA\n") | |
| 276 f.write("GAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATT\n") | |
| 277 f.write("TTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTA\n") | |
| 278 f.write("TATTTTCATACGGACGGACATGGCCAGATCAAAGACACTAGAATAACAAGATGCGTAACG\n") | |
| 279 f.write("CCATACGATTTTTTGGCACACAATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCT\n") | |
| 280 f.write("CTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACCGCTCTTTTCTA\n") | |
| 281 f.write("CGCATACAGTGATAGCAGACAACTTTATGTGCGCACACGTATGCTCATGCATTGTAAATT\n") | |
| 282 f.write("TGACAAAATATGCCCTTCACCGTAGAAGTTCTTAGACTTTAAATCTATATTATTTTTGAT\n") | |
| 283 f.write("CAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAA\n") | |
| 284 f.write("AATAGATTAGAAATAGCCAAATCTATGTACATAATATCACAAAAATAAATTTCAAAAATG\n") | |
| 285 f.write("ACTTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGGGTGTGAAAAATGAATA\n") | |
| 286 f.write("AGGCAATGATTGTTGCTTGTGTCCGTCCGCACTTCGTGCCTCAAGATATGACCAAAACAA\n") | |
| 287 f.write("AGACACTAGAATAATTCTAGTGTCTTTGATGTGACTTTTGCAATAAACAGTTTTCATATT\n") | |
| 288 f.write("TTTATTTATTTTACAAATTTTTATTTTCTACTTCGTATTATTTTTATGAAATATTTATTT\n") | |
| 289 f.write("CTCGATGTAATGTATTCCTTTTGTTATAAGTAGTTATAATAATTTATATTTTACTTCCTT\n") | |
| 290 f.write("CAATATCACAAAATAAATTTCAAGTATGGCTTTATATTAGAATAATTGTCATTAAATTAT\n") | |
| 291 f.write("TCAGCTTGGGACGTGGGAAAAATTAGAGTAGACATGTCTAGTAGACATCGATTCTTAGGT\n") | |
| 292 f.write("GCTTCTGACCGCACGTCGTGCCTCAAGAAATCAATTTCGCATATTTATACCCATTATTTC\n") | |
| 293 f.write("TAGAGTAAAAGGGTATACTACATTCGTTGAAAAGTATGTAACAGGCAGAAGAAAGCGTTT\n") | |
| 294 f.write("CCGACTATATAATGTATAAAGATCAGGATCAACAGCCGAGTCGATCTGGCCATGTCCGTC\n") | |
| 295 f.write("TGTCCGTATGAACGTCGAGGTCTCAGGAACTATAAAAGCAAGAAGGTAGAGATTATGCAT\n") | |
| 296 f.write("ACATATTATGCATACATATTGCCCGTTGACCCATGTTGTCACGCCCACTCTAACGTCCAC\n") | |
| 297 f.write("AAACCGCACAAAACTGCCACGCCCACAAATTCAAAAAATGTAAATGTAATTGACCAAATT\n") | |
| 298 f.write("TAACAAAACTCTAAAAATGTAACTTTGTTTCTTAGATCAAAATTTAGACCAGAAAATCGT\n") | |
| 299 f.write("CTTCATCTTCTAATGTTTTTACTCACACAAGAAAGCAAATTCTATTTTTAGATTTTAAAG\n") | |
| 300 f.write("TACTCCATTTTACGCGAGCGGAGAGAGAGAGCAATTTTGGCCGTCACCAAAAAAGTGTCT\n") | |
| 301 | |
| 302 | |
| 303 if __name__ == "__main__": | |
| 304 unittest.main() |