Mercurial > repos > yufei-luo > s_mart

from commons.core.seq.Bioseq import Bioseq
from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
from commons.core.sql.DbFactory import DbFactory
from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
from commons.core.sql.TablePathAdaptator import TablePathAdaptator
from commons.core.coord.Path import Path
import os
import unittest
from commons.tools.AlignTEOnGenomeAccordingToAnnotation import AlignTEOnGenomeAccordingToAnnotation

class Test_AlignTEOnGenomeAccordingToAnnotation(unittest.TestCase):

    def test_alignBioseqWithNWalign(self):
        iBioseq1 = Bioseq("dmel_chr4", "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAGTAGAAGAAA")
        iBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTTCTTCTACCTATTACATACTTTTCAACAAATCTAGCATACCCTTTTACTCTACGAGTA")
        iAlignedBioseq1 = Bioseq("dmel_chr4 Score=58 Identity=0.7", "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTT-TAGA-AGTACGTTACTAGTAGAAGAAA----------------------------")
        iAlignedBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat Score=58 Identity=0.7", "----------------------------TTTCTTCTACCTATTACAT-ACTTTTC-AACAAATCTAGCATACCCTTTTACTCTACGAGTA")
        expiAlignedBioseqDB = AlignedBioseqDB()
        expiAlignedBioseqDB.add(iAlignedBioseq1)
        expiAlignedBioseqDB.add(iAlignedBioseq2)

        iATEOGATA = AlignTEOnGenomeAccordingToAnnotation()
        obsiAlignedBioseqDB = iATEOGATA.alignBioseqWithNWalign(iBioseq1, iBioseq2)

        self.assertEquals(expiAlignedBioseqDB, obsiAlignedBioseqDB)

    def test_alignSeqAccordingToPathAndBuildAlignedSeqTable_one_path(self):
        iBioseq1 = Bioseq("dmel_chr4", "TTTCTTCTACTAGTAACGTACTTCTAAACAAATCTCTCATACCCTTTTCCTCTACGATTA")
        iBioseq2 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGATCAGTGTTTGTTGGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGATC")
        iPath = Path()
        iPath.setFromTuple((1, "dmel_chr4", 1, 60, "DmelChr4-B-R1-Map4_NoCat", 315, 256, 0, 249, 81.67))

        seqTable1 = "seqTable1_seq"
        seqTable2 = "seqTable2_seq"
        pathTable = "pathTable_path"

        iDb = DbFactory.createInstance()
        iDb.createTable(seqTable1, "seq", overwrite = True)
        iDb.createTable(seqTable2, "seq", overwrite = True)
        iDb.createTable(pathTable, "path", overwrite = True)

        iTSA1 = TableSeqAdaptator(iDb, seqTable1)
        iTSA2 = TableSeqAdaptator(iDb, seqTable2)
        iTPA = TablePathAdaptator(iDb, pathTable)
        iTSA1.insert(iBioseq1)
        iTSA2.insert(iBioseq2)
        iTPA.insert(iPath)

        expTTuples = ((1, "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAG-TAGAAGAAA", "TACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGT-AATAGGTAGAAGAAA", 406, 86.440700000000004),)

        iATEOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTable, seqTable1, seqTable2)
        iATEOGATA.setMergeSamePathId(True)
        iATEOGATA.setDbInstance(iDb)
        iATEOGATA.alignSeqAccordingToPathAndBuildAlignedSeqTable()

        #TODO: "select * from ..." + execute + fetchall => create method in TableAdaptator
        sqlCmd = "SELECT * FROM %s_align" % pathTable
        iDb.execute(sqlCmd)
        obsTTuples = iDb.fetchall()

        iDb.dropTable(seqTable1)
        iDb.dropTable(seqTable2)
        iDb.dropTable(pathTable)
        iDb.dropTable("%s_align" % pathTable)
        iDb.close()

        self.assertEquals(expTTuples, obsTTuples)

    def test_alignSeqAccordingToPathAndBuildAlignedSeqTable_n_paths(self):
        queryTableName = "query_seq"
        subjectTableName = "subject_seq"
        pathTableName = "table_path"

        iDb = DbFactory.createInstance()
        queryFileName = "dummyDmelChr4.fa"
        self._writeDummyDmelChr4(queryFileName)
        iDb.createTable(queryTableName, "seq", queryFileName, True)
        os.remove(queryFileName)
        iDb.createTable(subjectTableName, "seq", overwrite = True)
        iDb.createTable(pathTableName, "path", overwrite = True)

        iTSA = TableSeqAdaptator(iDb, subjectTableName)
        iTPA = TablePathAdaptator(iDb, pathTableName)
        iBioseq1 = Bioseq("DmelChr4-B-R1-Map4_NoCat", "TTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGATCAGTGTTTGTTGGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGATC")
        iBioseq2 = Bioseq("DmelChr4-B-R4-Map5_NoCat", "CCAAAATTGCCCTCTTTCCGCTCGCTCACGCTGAGAGCATAAGAAATCTAAAAATAGAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGTGTGCGTGTTGTGCTAGAAGACTATTTTCGGGCCGAAATCAATTCTGATCGAAAAAACGAATTTACATTGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAATAAAATAATTTTTAAAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTAAAATTTGTTTGTTAAAATCGCCGATCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATATTTTTTTTGAAACACTTTTAATGTTAAAAATGACTTAATAAATATACTAAATAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAAAATATGATAACTGTTTATTGCAAAAGTCATATCAAAGACACTAGAATTATTCTAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAAAGTCAAAGAACTTCTAAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACAGTTGTCTGCTATCACTTTATGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTCCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCGAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGGTA")
        iBioseq3 = Bioseq("DmelChr4-B-G9-Map3_NoCat", "ACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAAAAAAAAATTTTTTTTAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAAACACTTTTAATGTTAATGTTACATCATATTAAGTCAAATGATTTAATAAATATACTAAATAATTAAATATGATAACTGTTTATTGCAAAAGTAATATCAAAGACACTAGAATAATTCTAATGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCCCTCAACAATCATTGGCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGAAAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAACGTCTAAGAACTTCTGAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACATTTGTCTGCTATCACTTTGTGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACAAATGTATGTGTGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTCAGAAGTTCTTAGACGTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTTTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGCCAATGATTGTTGAGGGCTTGTGTCCGCACTTCGTGC")
        iTSA.insert(iBioseq1)
        iTSA.insert(iBioseq2)
        iTSA.insert(iBioseq3)
        iPath = Path()
        iPath.setFromTuple((1, "dmel_chr4", 1, 60, "DmelChr4-B-R1-Map4_NoCat", 315, 256, 0, 249, 81.67))
        iTPA.insert(iPath)
        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"
        iTPA.insert(iPath)
        iPath.setFromTuple((28, "dmel_chr4", 8971, 9459, "DmelChr4-B-G9-Map3_NoCat", 1102, 1590, 0, 758, 96.707800))
        iTPA.insert(iPath)
        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"
        iTPA.insert(iPath)
        iPath.setFromTuple((30, "dmel_chr4", 9957, 10047, "DmelChr4-B-G9-Map3_NoCat", 429, 337, 0, 33, 78.162700))
        iTPA.insert(iPath)
        iPath.setFromTuple((30, "dmel_chr4", 10094, 10127, "DmelChr4-B-G9-Map3_NoCat", 290, 256, 0, 13, 78.162700))
        iTPA.insert(iPath)

        expTTuples = ((1, "TAATCGTAGAGGAAAAGGGTATGAGAGATTTGTTTAGAAGTACGTTACTAG-TAGAAGAAA", "TACTCGTAGAGTAAAAGGGTATGCTAGATTTGTTGAAAAGTATGT-AATAGGTAGAAGAAA", 406, 86.440700000000004),\
                      (28, "CAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCGGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGAGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTATCAATATGATAAAATAAAAAAATTTTTAAAAATTCGCGCCCTGACTATTATAACTTGAAAGTTTTTTAAATTTGTTTGTTAAAAT-----------TT-------GTT---------------ATGTTTAATTCTAATTTGTCTGACAATCTGACATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAA-CACTTTTAATGTTAATGTTACATCATTTTAAGTCAAATGACTTATTAAATATACTAATTAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAA--AATATGATA---ACTAGAATTATTCCAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTCTTATATTTTTAAATAATAATAACGTTAAGGCAATGCAAA-CAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATACAGATTTAAAGTCTAAGAACTTCTAGGGTGAAGGGCTTTTTTTGTCAAATTTACAATGCATGAGCATTCGTGTGCACACATAAAGTTGTCTGCTATCACTGTATGCGTAGAAAAGAGCTGTTTGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACAATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACCGCTCTTTTCTACGCATACAGTGATAGCAGACAACTTTATGTGCGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCGTAGAAGTTCTTAGACTTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATAATATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGGGTGTGAAAAATGAATAAGGCAATGATTGTTG----CTTGTGTCCGTCCGCACTTCGTGC", "CAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATATGATAAAAAAAAAAATTTTTTTTAAATTCGCGCCCTGACTATTATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCT------CT--CATCTGACAATTTTTTAAAAGCGAAATATTTTTTTAAAACACTTTTAATGTTAATGTTACATCATATTAAGTCAAATGATTTAATAAATATACTAAATAATTAAA-----------------TATGATAACT---GT--TT------ATTGCA-AAAGTAATATCAAAGACACTAGAATAATTCTAATG------CTTTGTTCATATCTTGAGGCACGAAGTGCGGACACAAGCCCTCAACAATCATTGGCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGAAAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATATGTACATAGATTTGGCTATTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGCAAAACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATATAGATTTAACGTCTAAGAACTTCTGAGGTGAAGGGCATATTTTGTCAAATTTACAATGCATGAGCATACGTGTGCACACATACATTTGTCTGCTATCACTTTGTGCGTTGAAAAGAGCTGTTCGCTGTAGCGCTCTTCGCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCCAAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTGAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACAAATGTATGTGTGCACACGTATGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTCAGAAGTTCTTAGACGTTAAATCTATATTATTTTTGATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGCCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGACTTTATATAAGAATATTTTTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGCCAATGATTGTTGAGGGCTTGTGTCCG----CACTTCGTGC", 13732, 96.1763),\
                      (30, "------------------------------------ACATTTACAT-TTTTTGAATTTGTGGG-------CGTGGCA-GAACGGGCAATAT-GTATGCATA---ATATGTATGCATAATCTCTACCTTCTTGCTTTTATAGTTCCTGAGACCTCGACGTTCATACGGACAGACGAAATATGCGAAA", "ACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAATAATTTTAAAGCTTTTTAAATATGTTTGTTAAAATCGCCGCTCGAATTAGC--TACCGTTTACACATTTATATTTATGTTTAAT-TCTAATTTGTCAATATCAAAGAC-------------------------------------------", 158, 64.835200000000004))

        iATEOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTableName, queryTableName, subjectTableName)
        iATEOGATA.setMergeSamePathId(True)
        iATEOGATA.setDbInstance(iDb)
        iATEOGATA.alignSeqAccordingToPathAndBuildAlignedSeqTable()

        #TODO: "select * from ..." + execute + fetchall => create method in TableAdaptator
        sqlCmd = "SELECT * FROM %s_align" % pathTableName
        iDb.execute(sqlCmd)
        obsTTuples = iDb.fetchall()

        iDb.dropTable(queryTableName)
        iDb.dropTable(subjectTableName)
        iDb.dropTable(pathTableName)
        iDb.dropTable("%s_align" % pathTableName)
        iDb.close()

        self.assertEquals(expTTuples, obsTTuples)

    def _writeDummyDmelChr4(self, fileName):
        with open(fileName, "w") as f:
            f.write(">dmel_chr4\n")
            f.write("TTTCTTCTACTAGTAACGTACTTCTAAACAAATCTCTCATACCCTTTTCCTCTACGATTA\n")
            f.write("TGTTGGTATTAATGGTCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAG\n")
            f.write("AATTTCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAG\n")
            f.write("AAACTTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTAC\n")
            f.write("TTGTTAGTCTTAATAATACCCGTACTCGTAGAGTAAAAGCAAAGACACTAGAATAACAAG\n")
            f.write("ATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAA\n")
            f.write("ATTACTCTCTTTCGGCTCACTCCCGCTGAGAGCGTAAGAAATCTAAAAATATAATTTGCT\n")
            f.write("TGCTTGTGTGAGTAAAAACAAGAGACGAGAACGCGTATATGAGTGCGTGTTGTGCTAGAA\n")
            f.write("GACGATTTTCGGGCCGAAATCAATTCTGATCGAAGAAACGAATTTACATGGTACATATTA\n")
            f.write("GGGTAGTTTTTGCCAATTTCCTATCAATATGATAAAATAAAAAAATTTTTAAAAATTCGC\n")
            f.write("GCCCTGACTATTATAACTTGAAAGTTTTTTAAATTTGTTTGTTAAAATTTGTTATGTTTA\n")
            f.write("ATTCTAATTTGTCTGACAATCTGACATCTGACAATTTTTTAAAAGCGAAATATTTTTTTA\n")
            f.write("AACACTTTTAATGTTAATGTTACATCATTTTAAGTCAAATGACTTATTAAATATACTAAT\n")
            f.write("TAATTAAAGGAAGTACAATAGAAATTATTATAACTACTGTAATTTCATAAATTTCATAAA\n")
            f.write("AATATGATAACTAGAATTATTCCAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAGT\n")
            f.write("GCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAAT\n")
            f.write("ACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTTATTTTTGTGATAATAT\n")
            f.write("GTACATAGATTTGGCTATTTCTCTTATATTTTTAAATAATAATAACGTTAAGGCAATGCA\n")
            f.write("AACAAGAATTTTTCGCATGGTGCCAATTGATCAAAAATAATACAGATTTAAAGTCTAAGA\n")
            f.write("ACTTCTAGGGTGAAGGGCTTTTTTTGTCAAATTTACAATGCATGAGCATTCGTGTGCACA\n")
            f.write("CATAAAGTTGTCTGCTATCACTGTATGCGTAGAAAAGAGCTGTTTGCTGTAGCGCTCTTC\n")
            f.write("GCTCTCTCGCTCTCTAACAAAAATTCGAGAGAGCCTGGAGCCACCTCTAGAGCCACGGCC\n")
            f.write("AAAAAATCGTGTGCCAAAAAATCGTATGGCGTTACGCATCTTGTTATTCTAGTGTCTTTG\n")
            f.write("GTAAAATGGTATGCTAGATTTGTTGAAAAGTATGTAATAGGTAAAAGAAAGCGTTTTCGA\n")
            f.write("CCATATCAAGTATATATATATTTTTGATAAGGATTAATAGCCGAGTCGAAGTGGCCATGC\n")
            f.write("CATAGACGCATAGAAGCATAGACGCAGCGTAGAGATCCATGTTTCCCACTATAACGCCCA\n")
            f.write("CAAACCGCCCAAAATAAAATCGAAATGTTTCGATTTTTCTTTGTTTTATTGTTTGCCTTG\n")
            f.write("TCAATTTCTATGTATTTTATACCCAAAACACTTTGGCCAAGGCCAAGATGTAAGGAAGCA\n")
            f.write("TCTACAACACGCTTTTGAACACATCTTTTAATATCGCAGATAAATGATGAAATTTCTCGT\n")
            f.write("TCACATTTCCACTACCATTCCCCGGCTCAGGGGAAACTCAACCATAGCATTCTCTCTTGC\n")
            f.write("TTTGACTTCAGCATAGTGACGATAAGCACCAAGAGTCTGAATTATAAGTAGACTACCGTA\n")
            f.write("TAGGACTCATAAAACTGAAAAGCTGCTTTTATATTGCGATCAAAAAAGAAATTAATATTA\n")
            f.write("CGAAAATTGCTGTTGCTGGGGCAGGTGGATCAACATATCCCAACATATATTTAACTGTAT\n")
            f.write("TGCATTTTACCCTAAAATACGCTTTAATTAATGGTTTAAAAAAAACAGACTGTTTCTATT\n")
            f.write("TTCTATTTCTATTTATTTTATTCTTGGAAAGTTATTTTTTTAATTTTTTGACAAGAATCT\n")
            f.write("TTGAATTTACTTGCTTGCAATCCCACTAGCTAAGTGACGGGTATATAGAGTTTTCCCTTA\n")
            f.write("TTTTAATAATCTAGGGTCGCCAGTTTGTCCGTCAGTTCTTCGCTAACGAAGTTCGCTGTT\n")
            f.write("GGCTCGGTATCGACTGTGTAGTCTAGACTCCCTTCGTTGGTCCTCCTGCTGCGTTTCGTC\n")
            f.write("CTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAGTCTTCCTGGTGTGTAGGGTCTATTTTGT\n")
            f.write("TTCCATCTCTGAGTAAGTATAAATAAATTTGGCTTGATTTTTATACTTTAGAGAGCCGTA\n")
            f.write("ACGGATAATGAAATAACGCCCCCATACTCTAGATACAGTTTTATCAACAAAGAATTAACC\n")
            f.write("GTATATTGTAATTTGACAAAAATGTTGTATATTTTTCTTCGTAATAAGATCGATAGGGCA\n")
            f.write("TAGTTCTTATAATACAAAGCCGGCTTTTCTTACATACGTATAAGTCCATACATTTTTTAA\n")
            f.write("ACTAAAATTTATAATTTTTTTGACAATTGTAAATAAATTGTTATCTTGCTAAAAAATAAA\n")
            f.write("AAAGTTACAAAAATTTTTTAAAAATCATATTGATGTCAGCAATTAGATGTGCAATCACCA\n")
            f.write("TCTAGTGTAGCAGCAACATTTCCTAATTTTCGTGAAAGATGCATCTTTCGGCAATTAATA\n")
            f.write("TCAGTTTCAAGTGATTCCATAATCTTTAAACAAAGGTAAATAAGTGGATTAGACGAAAAA\n")
            f.write("AATTACGAAAATAGGTTAAATAGGTTACCTGATCCTTATATTTAGTTATATAAATGTATA\n")
            f.write("ACTCTTTTAATGCAGAAATAGTATCAAACTCTTCGTTTTGCCTTACTGATAGCTGTTGCA\n")
            f.write("TCGCTGTACTCATTTCCTGGTCGCTTATTTGTGGAAGCCTTGATACATCGCGGTAAAACT\n")
            f.write("CTTTGACCATAATTCTATAGTTTGGAATATCCTGTCATATAAACCAGTTAATTAAATATT\n")
            f.write("AATGATTTTATTAAAATATTTATACCATTACTTATAAATATTTAAATTTATTATTTGTGT\n")
            f.write("ATAAATTTGATAAAGGTAATAATCTAAGTAATATATACCAATATATATGCATATATGTAT\n")
            f.write("TCACATTTAAAAAAATGAAAGGGAAAAGAATTTGAAGTCTAATTGTATAAATTGTTTTTA\n")
            f.write("ATTTGTTTTATTCTCATTAGACCTCGATAATAGGTCTTTTGTGTGATTAATTAATTTGAT\n")
            f.write("AGACTCCTTACTTACAAGAAAAGAAGAAAACAGAAGGTTTACCAGGTGTTCCCTTTATCC\n")
            f.write("GTTACTCCAGTAAAGCGAGGGCGAACTAAATTTTTAAGCGTTGAAGAGGCCGTCTTGGTA\n")
            f.write("TTGGATCTTCCATGCTTAATGTCAACGTTCTATATTTTCATACGGACGGACATGGCCAGA\n")
            f.write("TCGACTCGCATATTGATGCTGATCAAGAATATTTATATTTTACATGATCGGAAACGCTTC\n")
            f.write("ATTGCTCTACGAGTAATGGGTACAATAATTTAAAACAAACATATTAAAAGTATAGCAAAA\n")
            f.write("CCCTATCTGAAGGACTAAAATTTTATCGCATTTTAAAATTTGTTGCATTAAAATCTTTGA\n")
            f.write("TAACCTTTCGTTGAATTAGGTGCTTCGACTTTTTTTACCCTAAGAACAATTTCGATTTGG\n")
            f.write("CATACATTGAAAACGTAGAAACTCAACCCTGCATTCATTCATAGAACTTATAAAGAGCTA\n")
            f.write("CATCTTCGAAAATAAAAAAAAGGTTTGTTTTTAAGACTTAATGCGTACAATGTCGCTTTC\n")
            f.write("GACATTAGGGTATTGCTAGAATTAATATTCGCTTTGTTGTTTACTTTTCCAAACAAACAT\n")
            f.write("AATGGGTAAACCAAAAAAATGGGAAACGTCAGTATTAAGTGCTATCGAAAACGTTTAGAA\n")
            f.write("TATGGAGAATCTAGTTGTTATTACCAAAACGCATAAATACTAAGCATATACTAAAACAAA\n")
            f.write("ATAGAAAAAGATAATGTTTATTTTAGACTCACCTTAGCAAACAGCAACTTATTCGACGGC\n")
            f.write("GAATCTTTTCCAAGTCTGTGCTCTGATGTTAAACAAGCGTCCATAAATGTTTGTGCAATG\n")
            f.write("ACACTTAAACAGGAATCAACGCTGTATGTTTTATTTACATCAAATATAAAATCCGGATTT\n")
            f.write("TTTATAAAATTAACCCAGAATCGAAGGGGCAAACAATTTGACTTCCAAGCGTGCACAATA\n")
            f.write("TCAGTATCAGCAATATCATGGCGTCGCGCAGCTTCATCAAGTAAGTCAAAGAGCCATTTA\n")
            f.write("ACGGCAGGTGGCAACTCCTCATTAACAGTTAAAATAATTGAGAAAAAATCATCAACAAAT\n")
            f.write("TTTTGTATAGTTCCTTTTGTGGCCAGAAGACGCGTAAGGTAAACTTCTGGTATTGTTTTG\n")
            f.write("TTCACCCTGTCATTACAATTATTAACGACATGCGATTGAAATGCTGGTGATCCTCCGGAT\n")
            f.write("AACACGGAATTTTTAATGTTCATATAATGATCAGGTATATTGGGCTTAACAAGATGGTAA\n")
            f.write("ACCCGGGGCTGCTGCAAACCTGATTCGATATCATTATTAATTATAATATGACTTTGCGAA\n")
            f.write("TTGTTTATAAAATAAACTGCAAAAAGGCAAAACAATTAATTAAAAAATTTTTAGATATTG\n")
            f.write("GGCTTAGTACTTACAATTGTGGTATGGTGCCGAATTTTGGTTTTTACTGTATGGTATATG\n")
            f.write("ATAATTATCATTTTGACGTGCAATTAGTGACATTACTGCAGATTCTTTGACTCCATAATG\n")
            f.write("AGCTAATGTGTTAAGGCGCTTCCATCCGTTAACGGTTTTGGTTGTCAAGTCTTCATCTTG\n")
            f.write("TAATGTAAGATGACCTCCTCGGCCGTGCCTCCATTCTAAGTCTACTTCGTTTACAGATGG\n")
            f.write("CCTCATAGAGAAAGGAGTGTTTTTAAAAATTGCGTCGAGGATTTTAAGCTTAACTTGAGA\n")
            f.write("AATGGTATCCCAATCGTTAACGCGACATTGGACTTTTTCATCAAGATCATCTTGTAAAAT\n")
            f.write("ATGCTATATTACAACAGAATGGGTAACTTGTTCATGCAGAAGACGTTCTTCTGAAAGGGA\n")
            f.write("GTAACGGGCATCGTTGGTTATTGCGTCCACTAAACCCTTTTCAATTTGATGCTTTATTGC\n")
            f.write("TTTGAAGAGCAAAAATAAATTTGATCCGGCGTACTCTTTCAGGTAATCGTACATACAAAT\n")
            f.write("TGCTAGGTAGTTGGTCAACATTTTTTCAACAACGCTTTCAGTACGCCTTAGCATCAGCTG\n")
            f.write("AGGATGTTTGCTGGCAAGTGATTTATCTATCAAACGTAATAAAAGGGACTTCAAAATTTC\n")
            f.write("CGTGGCATATTCCATCTTGTTCATTAAAACAACCATTATTAATGAGGCAACGTTAACTCG\n")
            f.write("GTCTCTAATAGAAAATGATGAACGTTGAGCTTCTAATGTTTCTATGAACATTAATAAAAA\n")
            f.write("ATATTTATTGCCAATCAGTTGTTCAAATTGTACCATAGCTGCGTCATAGTTAGTCTGTGG\n")
            f.write("GCTACCTTCACGAAATTTTGGAGAATTTAAAATAGGATGATCTGATACACCAGGGAAAAA\n")
            f.write("CACCTTCATAATATAGTTGACGTGATCTAAAGTTGGTATGCCTGTGCTCTCCAAATCTGC\n")
            f.write("TGTTAGGTCGGTCATGTCCGTTTGGAGCTCAGCGAATGCCTGTTTACACTCAGAACGTAC\n")
            f.write("GTTGCTTTCTAATGTAATCATCTGTATCTGAATACGTTTATACTCGCGTTCTGCTTGTGT\n")
            f.write("TGATTTCCTTCTGAATATTATAAGTACAATTACAAAAACAACGACCAGAAGTGCTACCGT\n")
            f.write("TAATATGCCGACTAACAAGGCATGTGAGAAAACATAGGGTTTATTTAAATCATACTTAAG\n")
            f.write("ATATCCTATTACAAAACGAAGATTTCGACCTACTTTAACGACAACAAGAGGTAAATCAGT\n")
            f.write("TGATTGATCCACACCATTTTCATCAGTTGGAAGTGGTTGTTGCTCCGGCGGAATGCATAA\n")
            f.write("AAGTTGGTTAAGTGCCAGGCTGGTAATATTGCATTGGGAAGTTCCAATAGTTACATTTAC\n")
            f.write("ATCGTACTCATCAGCTGCCAAGTTTAATAGCTCGCCTTCTATGACCAAGCTGTCACCCTT\n")
            f.write("GTAGAGTTTAACGCCGTCGTTGGGAAATGGCAAATATTTTGGGTCTGCTAAATAGACAAT\n")
            f.write("AGTGCTCCTTATGTCATGAAAATATTTATTCAAGTTTCGAACTAGTTGTACATTGTCCAT\n")
            f.write("TACAAAACTTAGTTGTAAGTTAAATTGAGTTTCATGAACCTTAACGAATGTGGTGACGTC\n")
            f.write("CATATTATTGTTAACAAAATAGTTGGCTGAAGATCCTGCATTTGTGTATAAGCGAAAAGT\n")
            f.write("GTCTCCAAAGTCGGCTCGCCGCTTTTTTCTATCATATTCATTTTTATACCTGGTTTCAGT\n")
            f.write("TTGAAACGAAGAATTTTGTAAGTGCAATTCAGTATCCATCTTTCTGTTCGTCTTTTTAAA\n")
            f.write("AGTCTCAAATTTTTAATTTACCGGAGGAGATGGACATTCCATTTGATTAGAGTTGATCAC\n")
            f.write("CACACAAGATGTTTTATTTACTCTTTCATTGTCATAAAACACTTCTAGTTCAGGTTTTTG\n")
            f.write("GTTTTATTTGTCTCCGAACTTCTTACTGACAATGGCACCAAAATATGTTCAGTGTTTGTT\n")
            f.write("GGTATTAATGGCCTTTCATCTAATGGGGGAGTAGCACATCCGAGTCCGTTTTCCAGAATT\n")
            f.write("TCGGCATCAATGGGGGTGGAATTTCCAAAAACACATCGGTATTTTGCAAGAACAAGAAAC\n")
            f.write("TTATTATTAATTACAGCTATGTATCCAGTTACACCAATAAATTTCCGTCGCCGTACTTGT\n")
            f.write("TAGTCTTAATAATACCCGTACTTGTAGAGTAAAAGGGTATGCTAGATTTGTAGAAAAGTA\n")
            f.write("TGTAATAGGTAGAAGAAAGCGTTTTCGACCATATCAAGTATATATATATTTTTGATAAGG\n")
            f.write("ATTAATAGCCGAGTCGAAGTGGCCATGCCATAGACGCATAGAAGCATAGACGCAGCGTAG\n")
            f.write("AGATCCATGTTTCCCACTATAACGCCCACAAACCGCCCAAAATAAAATCGAAATGTTTCG\n")
            f.write("ATTTTTCTTTGTTTTATTGTTTGCCTTGTCAATTTCTATGTATTTTATACCCAAAACACT\n")
            f.write("TTGGCCAAGGCCAAGATGTAAGGAAGCATCTACAACACGCTTTTGAACACATCTTTTAAT\n")
            f.write("ATCGCAGATAAATGATGAAATTTCTCGTTCACATTTCCACTACCATTCCCCGGCTCAGGG\n")
            f.write("GAAACTCAACCATAACATTCTCTCTTGCTTTGACTTCAGCATAGTGACGATAAGCACCAA\n")
            f.write("GAGTCTGAATTATAAGTAGACTACCGTATAGGACTCATAAAACTGAAAAGCTGCTTTTAT\n")
            f.write("ATTGCGATCAAAAAAGAAATTAATATTACGAAAATTGCTGTTGCTGGGGCAGGTGGATCA\n")
            f.write("ACATATCCCAACATATATTTAACTGTATTGCATTTTACCCTAAAATACGCTTTAATTAAT\n")
            f.write("GGTTTAAAAAAAACAGACTGTTTCTATTTTCTATTTCTATTTATTTTATTCTTGGAAAGT\n")
            f.write("TATTTTTTTAATTTTTTGACAAGAATCTTTGAATTTACTTGCTTGCAATCCCACTAGCTA\n")
            f.write("AGTGACGGGTATATAGAGTTTTCCCTTATTTTAATAATCTAGGGTCGCCAGTTTGTCCGT\n")
            f.write("CAGTTCTTCGCTAACGAAGTTCGCTGTTGGCTCGGTATCGACTGTGTAGTCTAGACTCCC\n")
            f.write("TTCGTTGGTCCTCCTGCTGCGTTTCGTCCTTGCTAAGGGCTTTGCCCTCTGGCTTCGTAG\n")
            f.write("TCTTCCTGGTGTGTAGGGTCTATTTTGTTTCCATCTCTGAGTAAGTATAAATAAATTTGG\n")
            f.write("CTTGATTTTTATACTTTAGAGAGCCGTAACGGATAATGAAATAACGCCCCCATACTCTAG\n")
            f.write("ATATAGTTTTATCAACAAAGAATTAACCGTATATTGTAATTTGACAAAAATGTTGTATAT\n")
            f.write("TTTTCTTCGTAATAAGATCGATAGGGCATAGTTCTTATAATACAAAGCCGGCTTCTCTTA\n")
            f.write("CATACGTATAAGTCCATACATTTTTTAAACTAAAATTTATAATTTTTTTGACAATTGTAA\n")
            f.write("ATAAATTGTTATCTTGCTAAAAAATAAAAAAGTTACAAAAATTTTTAAAAAATCATATTG\n")
            f.write("ATGTCAGCAATTAGATGTGCAATCACCATCTAGTGTAGCAGCAACATTTCCTAATTTTCG\n")
            f.write("TGAAAGATGCATCTTTCGGCAATTAATATCAGTTTCAAGTGATTCCATAATCTTTAAACA\n")
            f.write("AAGGTAAATAAGTGGATTAGACGAAAAAAATTACGAAAATAGGTTAAATAGGTTACCTGA\n")
            f.write("TCCTTATATTTAGTTATATAAATGTATAACTCTTTTAATGCAGAAATAGTATCAAACTCT\n")
            f.write("TCGTTTTGCCTTACTGATAGCTGTTGCATAGCTGTACTCATTTCCTGGTCGCTTATTTGT\n")
            f.write("GGAAGCCTTGATACATCGCGGTAAAACTCTTTGACCATAATTCTATAGTTTGGAATATCC\n")
            f.write("TGTCATATAAACCAGTTAATTAAATATTAATGATTTTATTAAAATATTTATACCATTACT\n")
            f.write("TATAAATATTTAAATTTATTATTTGTGTATAAATTTGATAAAGGTAATAATCTAAGTAAT\n")
            f.write("ATATACCAATATATATGCATATATGTATTCACATTTAAAAAAATGAAAGGGAAAAGAATT\n")
            f.write("TGAAGTCTAATTGTATAAATTGTTTTTAATTTGTTTTATTCTCATTAGACCTCGATAATA\n")
            f.write("GGTCTTTTGTGTGATTAATTAATTTGATAGACTCCTTACTTACAAGAAAAGAAGAAAACA\n")
            f.write("GAAGGTTTACCAGGTGTTCCCTTTATCCGTTACTCCAGTAAAGCGAGGGCGAACTAAATT\n")
            f.write("TTTAAGCGTTGAAGAGGCCGTCTTGGTATTGGATCTTCCATGCTTAATGTCAACGTTCTA\n")
            f.write("TATTTTCATACGGACGGACATGGCCAGATCAAAGACACTAGAATAACAAGATGCGTAACG\n")
            f.write("CCATACGATTTTTTGGCACACAATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCT\n")
            f.write("CTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACCGCTCTTTTCTA\n")
            f.write("CGCATACAGTGATAGCAGACAACTTTATGTGCGCACACGTATGCTCATGCATTGTAAATT\n")
            f.write("TGACAAAATATGCCCTTCACCGTAGAAGTTCTTAGACTTTAAATCTATATTATTTTTGAT\n")
            f.write("CAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAA\n")
            f.write("AATAGATTAGAAATAGCCAAATCTATGTACATAATATCACAAAAATAAATTTCAAAAATG\n")
            f.write("ACTTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGGGTGTGAAAAATGAATA\n")
            f.write("AGGCAATGATTGTTGCTTGTGTCCGTCCGCACTTCGTGCCTCAAGATATGACCAAAACAA\n")
            f.write("AGACACTAGAATAATTCTAGTGTCTTTGATGTGACTTTTGCAATAAACAGTTTTCATATT\n")
            f.write("TTTATTTATTTTACAAATTTTTATTTTCTACTTCGTATTATTTTTATGAAATATTTATTT\n")
            f.write("CTCGATGTAATGTATTCCTTTTGTTATAAGTAGTTATAATAATTTATATTTTACTTCCTT\n")
            f.write("CAATATCACAAAATAAATTTCAAGTATGGCTTTATATTAGAATAATTGTCATTAAATTAT\n")
            f.write("TCAGCTTGGGACGTGGGAAAAATTAGAGTAGACATGTCTAGTAGACATCGATTCTTAGGT\n")
            f.write("GCTTCTGACCGCACGTCGTGCCTCAAGAAATCAATTTCGCATATTTATACCCATTATTTC\n")
            f.write("TAGAGTAAAAGGGTATACTACATTCGTTGAAAAGTATGTAACAGGCAGAAGAAAGCGTTT\n")
            f.write("CCGACTATATAATGTATAAAGATCAGGATCAACAGCCGAGTCGATCTGGCCATGTCCGTC\n")
            f.write("TGTCCGTATGAACGTCGAGGTCTCAGGAACTATAAAAGCAAGAAGGTAGAGATTATGCAT\n")
            f.write("ACATATTATGCATACATATTGCCCGTTGACCCATGTTGTCACGCCCACTCTAACGTCCAC\n")
            f.write("AAACCGCACAAAACTGCCACGCCCACAAATTCAAAAAATGTAAATGTAATTGACCAAATT\n")
            f.write("TAACAAAACTCTAAAAATGTAACTTTGTTTCTTAGATCAAAATTTAGACCAGAAAATCGT\n")
            f.write("CTTCATCTTCTAATGTTTTTACTCACACAAGAAAGCAAATTCTATTTTTAGATTTTAAAG\n")
            f.write("TACTCCATTTTACGCGAGCGGAGAGAGAGAGCAATTTTGGCCGTCACCAAAAAAGTGTCT\n")


if __name__ == "__main__":
    unittest.main()
author	m-zytnicki
date	Mon, 29 Apr 2013 03:20:15 -0400
parents
children