Mercurial > repos > yufei-luo > s_mart
view commons/core/seq/test/Test_Bioseq.py @ 16:6135c3075bc5
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author | m-zytnicki |
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date | Mon, 22 Apr 2013 11:09:41 -0400 |
parents | 769e306b7933 |
children | 94ab73e8a190 |
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# Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. import unittest import os import sys from commons.core.seq.Bioseq import Bioseq from commons.core.utils.FileUtils import FileUtils from commons.core.coord.Map import Map class Test_Bioseq( unittest.TestCase ): def setUp(self): self._bs = Bioseq() def test_isEmpty_True(self): self._bs.setHeader( "" ) self._bs.setSequence( "" ) exp = True obs = self._bs.isEmpty() self.assertEquals( exp, obs ) def test_isEmpty_False(self): self._bs.setHeader( "seq1" ) self._bs.setSequence( "AGCGGACGATGCAGCATGCGAATGACGAT" ) exp = False obs = self._bs.isEmpty() self.assertEquals( exp, obs ) def test___eq__(self): self._bs.setHeader( "seq1" ) self._bs.setSequence( "AGCGGACGATGCAGCATGCGAATGACGAT" ) obs = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) self.assertEquals( self._bs, obs ) def test___ne__Header(self): self._bs.setHeader( "seq2" ) self._bs.setSequence( "AGCGGACGATGCAGCATGCGAATGACGAT" ) obs = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) self.assertNotEquals( self._bs, obs ) def test___ne__Sequence(self): self._bs.setHeader( "seq1" ) self._bs.setSequence( "GGACGATGCAGCATGCGAATGACGAT" ) obs = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) self.assertNotEquals( self._bs, obs ) def test_reverse(self): self._bs.setHeader( "seq1" ) self._bs.setSequence( "TGCGGA" ) exp = "AGGCGT" self._bs.reverse() obs = self._bs.sequence self.assertEqual( obs, exp ) def test_complement(self): self._bs.setHeader( "seq1" ) self._bs.setSequence( "TGCGGA" ) exp = "ACGCCT" self._bs.complement() obs = self._bs.sequence self.assertEqual( obs, exp ) def test_complement_with_unknown_symbol(self): self._bs.setHeader( "seq1" ) self._bs.setSequence( "TGCGGAFMRWTYSKVHDBN" ) exp = "ACGCCTNKYWARSMBDHVN" self._bs.complement() obs = self._bs.sequence self.assertEqual( obs, exp ) def test_reverseComplement(self): self._bs.setHeader( "seq1" ) self._bs.setSequence( "TGCGGA" ) exp = "TCCGCA" self._bs.reverseComplement() obs = self._bs.sequence self.assertEqual( obs, exp ) def test_cleanGap(self): self._bs.setSequence("-ATTTTGC-AGTC--TTATTCGAG-----GCCATTGCT-") exp = "ATTTTGCAGTCTTATTCGAGGCCATTGCT" self._bs.cleanGap() obs = self._bs.sequence self.assertEquals( obs, exp ) def test_copyBioseqInstance(self): self._bs.setHeader( "seq" ) self._bs.setSequence( "TGCGGA" ) obsBioseq = self._bs.copyBioseqInstance() self.assertEquals(self._bs, obsBioseq) def test_setFrameInfoOnHeader_without_description(self): self._bs.setHeader( "seq" ) self._bs.setSequence( "TGCGGA" ) phase = -1 expHeader = "seq_-1" self._bs.setFrameInfoOnHeader(phase) self.assertEquals(expHeader, self._bs.header) def test_setFrameInfoOnHeader_with_description(self): self._bs.setHeader( "seq description" ) self._bs.setSequence( "TGCGGA" ) phase = -1 expHeader = "seq_-1 description" self._bs.setFrameInfoOnHeader(phase) self.assertEquals(expHeader, self._bs.header) def test_read(self): faFile = open("dummyFaFile.fa", "w") faFile.write(">seq1 description1\n") faFile.write("ATGCGTCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") faFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") faFile.close() expBioseq = Bioseq() expBioseq.header = "seq1 description1" expBioseq.sequence = "ATGCGTCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" obsBioseq = Bioseq() faFile = open("dummyFaFile.fa", "r") obsBioseq.read( faFile ) faFile.close() os.remove("dummyFaFile.fa") self.assertEquals(expBioseq, obsBioseq) def test_read_WithEmptyFile(self): faFile = open("dummyFaFile.fa", "w") faFile.close() expBioseq = Bioseq() expBioseq.header = None expBioseq.sequence = None obsBioseq = Bioseq() faFile = open("dummyFaFile.fa", "r") obsBioseq.read( faFile ) faFile.close() os.remove("dummyFaFile.fa") self.assertEquals(expBioseq, obsBioseq) def test_read_without_header(self): faFile = open("dummyFaFile.fa", "w") faFile.write("seq1 description1\n") faFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") faFile.close() expBioseq = Bioseq() expBioseq.header = "" expBioseq.sequence = "" obsBioseq = Bioseq() faFile = open("dummyFaFile.fa", "r") obsBioseq.read( faFile ) faFile.close() os.remove("dummyFaFile.fa") self.assertEquals(expBioseq, obsBioseq) def test_read_with_two_consecutive_headers(self): faFile = open("dummyFaFile.fa", "w") faFile.write(">seq1 description1\n") faFile.write(">ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") faFile.close() expBioseq = Bioseq() expBioseq.header = "seq1 description1" expBioseq.sequence = "" obsBioseq = Bioseq() faFile = open("dummyFaFile.fa", "r") obsBioseq.read( faFile ) faFile.close() os.remove("dummyFaFile.fa") self.assertEquals(expBioseq, obsBioseq) def test_read_withEmptyLines(self): faFile = open("dummyFaFile.fa", "w") faFile.write("\n") faFile.write(">seq1 description1\n") faFile.write("ATGCGTCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") faFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") faFile.write("\n") faFile.close() exp = Bioseq( "seq1 description1", "ATGCGTCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" ) obs = Bioseq() faFile = open("dummyFaFile.fa", "r") obs.read( faFile ) faFile.close() os.remove("dummyFaFile.fa") self.assertEquals( exp, obs ) def test_read_with_70nt_by_line(self): faFile = open("dummyFaFile.fa", "w") faFile.write("\n") faFile.write(">seq1 description1\n") faFile.write("TGTCACATCCTGATTTTCGTTTCAGGATTTATAAATTATTTAATAAATTAATAATAGAATTTATATTAAA\n") faFile.write("TGTTTTTTAATTTACAAGTGAAGTTAAATGTGGGAAATAAAATTTCTTAAATCTAAAGCATGGATGGATT\n") faFile.write("\n") faFile.close() exp = Bioseq( "seq1 description1", "TGTCACATCCTGATTTTCGTTTCAGGATTTATAAATTATTTAATAAATTAATAATAGAATTTATATTAAATGTTTTTTAATTTACAAGTGAAGTTAAATGTGGGAAATAAAATTTCTTAAATCTAAAGCATGGATGGATT" ) obs = Bioseq() faFile = open("dummyFaFile.fa", "r") obs.read( faFile ) faFile.close() os.remove("dummyFaFile.fa") self.assertEquals( exp, obs ) def test_appendBioseqInFile(self): obsFaFileName = "dummyFaFile.fa" obsFaFile = open(obsFaFileName, "w") obsFaFile.write(">seq1 description1\n") obsFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") obsFaFile.close() bioseq = Bioseq() bioseq.header = "seq2 description2" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expFaFileName = "dummyFaFile2.fa" expFaFile = open(expFaFileName, "w") expFaFile.write(">seq1 description1\n") expFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") expFaFile.write(">seq2 description2\n") expFaFile.write("GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFaFile.write("ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFaFile.write("ATAGCAGACGCATATTATATTGCGCG\n") expFaFile.close() bioseq.appendBioseqInFile(obsFaFileName) self.assertTrue(FileUtils.are2FilesIdentical(expFaFileName, obsFaFileName)) os.remove(obsFaFileName) os.remove(expFaFileName) def test_writeABioseqInAFastaFile(self): obsFaFileName = "dummyFaFile.fa" obsFaFile = open(obsFaFileName, "w") obsFaFile.write(">seq1 description1\n") obsFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") bioseq = Bioseq() bioseq.header = "seq2 description2" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expFaFileName = "dummyFaFile2.fa" expFaFile = open(expFaFileName, "w") expFaFile.write(">seq1 description1\n") expFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") expFaFile.write(">seq2 description2\n") expFaFile.write("GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFaFile.write("ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFaFile.write("ATAGCAGACGCATATTATATTGCGCG\n") expFaFile.close() bioseq.writeABioseqInAFastaFile(obsFaFile) obsFaFile.close() self.assertTrue(FileUtils.are2FilesIdentical(expFaFileName, obsFaFileName)) os.remove(obsFaFileName) def test_writeABioseqInAFastaFileWithOtherHeader(self): obsFaFileName = "dummyFaFile.fa" obsFaFile = open(obsFaFileName, "w") obsFaFile.write(">seq1 description1\n") obsFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") bioseq = Bioseq() bioseq.header = "seq2 description2" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expFaFileName = "dummyFaFile2.fa" newHeader = "seq2 New header2" expFaFile = open(expFaFileName, "w") expFaFile.write(">seq1 description1\n") expFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") expFaFile.write(">" + newHeader + "\n") expFaFile.write("GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFaFile.write("ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFaFile.write("ATAGCAGACGCATATTATATTGCGCG\n") expFaFile.close() bioseq.writeABioseqInAFastaFileWithOtherHeader(obsFaFile, newHeader) obsFaFile.close() self.assertTrue(FileUtils.are2FilesIdentical(expFaFileName, obsFaFileName)) os.remove(obsFaFileName) os.remove(expFaFileName) def test_writeSeqInFasta(self): iBs = Bioseq() iBs.header = "dummySeq" iBs.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expFaFile = "dummyExpFile.fa" expFaFileHandler = open(expFaFile, "w") expFaFileHandler.write("GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFaFileHandler.write("ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFaFileHandler.write("ATAGCAGACGCATATTATATTGCGCG\n") expFaFileHandler.close() obsFaFile = "dummyObsFile.fa" obsFaFileHandler = open( obsFaFile, "w" ) iBs.writeSeqInFasta( obsFaFileHandler ) obsFaFileHandler.close() self.assertTrue( FileUtils.are2FilesIdentical( expFaFile, obsFaFile ) ) os.remove(obsFaFile) os.remove(expFaFile) def test_subseq(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" start = 10 end = 30 expSubBioseq = Bioseq() expSubBioseq.header = "seq1 description1 fragment " + str(start) + ".." + str(end) expSubBioseq.sequence = bioseq.sequence[(start - 1) : end] obsBioseq = bioseq.subseq(start, end) self.assertEquals(expSubBioseq, obsBioseq) def test_subseq_no_end(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" start = 10 expSubBioseq = Bioseq() expEnd = len(bioseq.sequence) expSubBioseq.header = "seq1 description1 fragment " + str(start) + ".." + str(expEnd) expSubBioseq.sequence = bioseq.sequence[(start - 1) : expEnd] obsBioseq = bioseq.subseq(start) self.assertEquals(expSubBioseq, obsBioseq) def test_subseq_start_gt_end(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" start = 30 end = 10 expSubBioseq = None obsBioseq = bioseq.subseq(start, end) self.assertEquals(expSubBioseq, obsBioseq) def test_subseq_start_eq_end(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" start = 10 end = 10 expSubBioseq = Bioseq() expSubBioseq.header = "seq1 description1 fragment " + str(start) + ".." + str(end) expSubBioseq.sequence = bioseq.sequence[(start - 1) : end] obsBioseq = bioseq.subseq(start, end) self.assertEquals(expSubBioseq, obsBioseq) def test_subseq_negative_start(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" start = -10 end = 10 expSubBioseq = None obsBioseq = bioseq.subseq(start, end) self.assertEquals(expSubBioseq, obsBioseq) def test_getNtFromPosition_1(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expNt = "G" obsNt = bioseq.getNtFromPosition(1) self.assertEquals(expNt, obsNt) def test_getNtFromPosition_10(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expNt = "C" obsNt = bioseq.getNtFromPosition(10) self.assertEquals(expNt, obsNt) def test_getNtFromPosition_last(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expNt = "G" obsNt = bioseq.getNtFromPosition(146) self.assertEquals(expNt, obsNt) def test_getNtFromPosition_position_outside_range_0(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expNt = None obsNt = bioseq.getNtFromPosition(0) self.assertEquals(expNt, obsNt) def test_getNtFromPosition_position_outside_range_negative(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expNt = None obsNt = bioseq.getNtFromPosition(-10) self.assertEquals(expNt, obsNt) def test_getNtFromPosition_position_outside_range_positive(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expNt = None obsNt = bioseq.getNtFromPosition(147) self.assertEquals(expNt, obsNt) def test_view(self): obsFileName = "obsdummy_Bioseq_view" expFileName = "expDummy_Bioseq_View" bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" obsFile = open(obsFileName,"w") expFile = open(expFileName, "w") expFile.write ( ">seq1 description1\n") expFile.write ( "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFile.write ( "ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFile.write ( "ATAGCAGACGCATATTATATTGCGCG\n") stdoutRef = sys.stdout sys.stdout = obsFile bioseq.view() obsFile.close() expFile.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) sys.stdout = stdoutRef os.remove ( obsFileName ) os.remove ( expFileName ) def test_view_with_l(self): obsFileName = "obsdummy_Bioseq_view" expFileName = "expDummy_Bioseq_View" bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" obsFile = open(obsFileName,"w") expFile = open(expFileName, "w") expFile.write ( ">seq1 description1\n") expFile.write ( "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") expFile.write ( "ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") stdoutRef = sys.stdout sys.stdout = obsFile bioseq.view(120) obsFile.close() expFile.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) sys.stdout = stdoutRef os.remove ( obsFileName ) os.remove ( expFileName ) def test_getLength(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expLength = 146 obsLength = bioseq.getLength() self.assertEquals(expLength, obsLength) def test_getLength_empty_seq(self): bioseq = Bioseq() expLength = 0 obsLength = bioseq.getLength() self.assertEquals(expLength, obsLength) def test_getLength_WithoutN(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGANCGCTGCTTTATTAAGCGCTAGATGNNNNNNNNNNNNNNNCGACGCTGCATTTATTAAGCGCTAGCGATTATANNNNNNNNNTAGCAGACGCATATTATATTGCGCGATGCGACGCTGCTTTATTANAGCGCTAGCGNNATTATATAGCANGACGCATATTATATTGCGCG" expLength = 146 obsLength = bioseq.getLength(False) self.assertEquals(expLength, obsLength) def test_getLength_WithoutN_empty_seq(self): bioseq = Bioseq() expLength = 0 obsLength = bioseq.getLength(False) self.assertEquals(expLength, obsLength) def test_countNt(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expCount = 3 obsCount = bioseq.countNt('N') self.assertEquals(expCount, obsCount) def test_countNt_withCharacterNotExisting(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" expCount = 0 obsCount = bioseq.countNt('W') self.assertEquals(expCount, obsCount) def test_countAllNt(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" dExpCount = {'A': 34, 'C': 31, 'T': 43, 'G': 35, 'N': 3} dObsCount = bioseq.countAllNt() self.assertEquals(dExpCount, dObsCount) def test_occ_word_size_1(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" dExpOccWord = {'A': 34, 'C': 31, 'T': 43, 'G': 35} ExpNbWord = 143 dObsOccWord, ObsNbWord = bioseq.occ_word(1) self.assertEquals(dExpOccWord, dObsOccWord) self.assertEquals(ExpNbWord, ObsNbWord) def test_occ_word_size_0(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" dExpOccWord = {} ExpNbWord = 0 dObsOccWord, ObsNbWord = bioseq.occ_word(0) self.assertEquals(dExpOccWord, dObsOccWord) self.assertEquals(ExpNbWord, ObsNbWord) def test_occ_word_size_n(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" dExpOccWord = {'ACC': 0, 'ATG': 2, 'AAG': 3, 'AAA': 0, 'ATC': 0, 'AAC': 0, 'ATA': 8, 'AGG': 0, 'CCT': 0, 'CTC': 0, 'AGC': 8, 'ACA': 0, 'AGA': 2, 'CAT': 3, 'AAT': 0, 'ATT': 9, 'CTG': 3, 'CTA': 3, 'ACT': 0, 'CAC': 0, 'ACG': 2, 'CAA': 0, 'AGT': 0, 'CAG': 2, 'CCG': 0, 'CCC': 0, 'CTT': 3, 'TAT': 13, 'GGT': 0, 'TGT': 0, 'CGA': 3, 'CCA': 0, 'TCT': 0, 'GAT': 3, 'CGG': 0, 'TTT': 3, 'TGC': 7, 'GGG': 0, 'TAG': 5, 'GGA': 0, 'TAA': 3, 'GGC': 0, 'TAC': 0, 'TTC': 0, 'TCG': 0, 'TTA': 10, 'TTG': 2, 'TCC': 0, 'GAA': 0, 'TGG': 0, 'GCA': 5, 'GTA': 0, 'GCC': 0, 'GTC': 0, 'GCG': 12, 'GTG': 0, 'GAG': 0, 'GTT': 0, 'GCT': 9, 'TGA': 0, 'GAC': 2, 'CGT': 0, 'TCA': 0, 'CGC': 10} ExpNbWord = 135 dObsOccWord, ObsNbWord = bioseq.occ_word(3) self.assertEquals(dExpOccWord, dObsOccWord) self.assertEquals(ExpNbWord, ObsNbWord) def test_freq_word_size_1(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" dExpFreqWord = {'A': 0.23776223776223776, 'C': 0.21678321678321677, 'T': 0.30069930069930068, 'G': 0.24475524475524477} dObsFreqWord = bioseq.freq_word(1) self.assertEquals(dExpFreqWord, dObsFreqWord) def test_freq_word_size_0(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" dExpFreqWord = {} dObsFreqWord = bioseq.freq_word(0) self.assertEquals(dExpFreqWord, dObsFreqWord) def test_freq_word_size_n(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" dExpFreqWord = {'ACC': 0.0, 'ATG': 0.014814814814814815, 'AAG': 0.022222222222222223, 'AAA': 0.0, 'ATC': 0.0, 'AAC': 0.0, 'ATA': 0.059259259259259262, 'AGG': 0.0, 'CCT': 0.0, 'CTC': 0.0, 'AGC': 0.059259259259259262, 'ACA': 0.0, 'AGA': 0.014814814814814815, 'CAT': 0.022222222222222223, 'AAT': 0.0, 'ATT': 0.066666666666666666, 'CTG': 0.022222222222222223, 'CTA': 0.022222222222222223, 'ACT': 0.0, 'CAC': 0.0, 'ACG': 0.014814814814814815, 'CAA': 0.0, 'AGT': 0.0, 'CAG': 0.014814814814814815, 'CCG': 0.0, 'CCC': 0.0, 'TAT': 0.096296296296296297, 'GGT': 0.0, 'TGT': 0.0, 'CGA': 0.022222222222222223, 'CCA': 0.0, 'TCT': 0.0, 'GAT': 0.022222222222222223, 'CGG': 0.0, 'CTT': 0.022222222222222223, 'TGC': 0.05185185185185185, 'GGG': 0.0, 'TAG': 0.037037037037037035, 'GGA': 0.0, 'TAA': 0.022222222222222223, 'GGC': 0.0, 'TAC': 0.0, 'TTC': 0.0, 'TCG': 0.0, 'TTT': 0.022222222222222223, 'TTG': 0.014814814814814815, 'TCC': 0.0, 'GAA': 0.0, 'TGG': 0.0, 'GCA': 0.037037037037037035, 'GTA': 0.0, 'GCC': 0.0, 'GTC': 0.0, 'TGA': 0.0, 'GCG': 0.088888888888888892, 'GTG': 0.0, 'GAG': 0.0, 'GTT': 0.0, 'GCT': 0.066666666666666666, 'TTA': 0.07407407407407407, 'GAC': 0.014814814814814815, 'CGT': 0.0, 'TCA': 0.0, 'CGC': 0.07407407407407407} dObsFreqWord = bioseq.freq_word(3) self.assertEquals(dExpFreqWord, dObsFreqWord) def test_findORF_no_ORF_in_sequence (self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "GCGNCGCTGCTTTATT" expORF = {0:[],1:[],2:[]} obsORF = bioseq.findORF() self.assertEquals (expORF,obsORF) def test_findORF_one_ORF_in_first_phase(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "TAAGCGNCGCTGCTTTATT" expORF = {0:[0],1:[],2:[]} obsORF = bioseq.findORF() self.assertEquals (expORF,obsORF) def test_findORF_three_ORF_in_first_phase(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "TAAGCGTAGNCGTGACTGCTTTATT" expORF = {0:[0,6,12],1:[],2:[]} obsORF = bioseq.findORF() self.assertEquals (expORF,obsORF) def test_findORF_two_ORF_in_first_phase_one_ORF_in_second_phase(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "TAAGTAGAGNCGTGACTGCTTTATT" expORF = {0:[0,12],1:[4],2:[]} obsORF = bioseq.findORF() self.assertEquals (expORF,obsORF) def test_findORF_two_ORF_in_first_phase_three_ORF_in_second_phase(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "TAAGTAGAGNCGTGACTGATAGTATT" expORF = {0:[0,12],1:[4,16,19],2:[]} obsORF = bioseq.findORF() self.assertEquals (expORF,obsORF) def test_findORF_one_ORF_in_second_phase_three_ORF_in_third_phase(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "AATATTAGTGGAGTAGTTGATGATTTT" expORF = {0:[], 1:[13], 2:[5,17,20]} obsORF = bioseq.findORF() self.assertEquals (expORF,obsORF) def test_findORF_three_ORF_in_second_phase_one_ORF_in_third_phase(self): bioseq = Bioseq() bioseq.header = "seq1 description1" bioseq.sequence = "TTTGAAGTGGAGGAGTTGATGATTTTAAT" expORF = {0:[], 1:[16, 19, 25], 2:[2]} obsORF = bioseq.findORF() self.assertEquals (expORF,obsORF) def test_upCase(self): bioseq = Bioseq() bioseq.header = "seq description" bioseq.sequence = "taattcggcct" expSeq = "TAATTCGGCCT" bioseq.upCase() obsSeq = bioseq.sequence self.assertEquals( expSeq, obsSeq ) def test_lowCase(self): bioseq = Bioseq() bioseq.header = "seq description" bioseq.sequence = "TAATTCGGCCT" expSeq = "taattcggcct" bioseq.lowCase() obsSeq = bioseq.sequence self.assertEquals( expSeq, obsSeq ) def test_getClusterID(self): bioseq = Bioseq() bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74091..74624" bioseq.sequence = "TAATTCGGCCT" expID = "0" obsID = bioseq.getClusterID() self.assertEquals( expID, obsID ) def test_getGroupID(self): bioseq = Bioseq() bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74091..74624" bioseq.sequence = "TAATTCGGCCT" expID = "2" obsID = bioseq.getGroupID() self.assertEquals( expID, obsID ) def test_getHeaderFullSeq(self): bioseq = Bioseq() bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74091..74624" bioseq.sequence = "TAATTCGGCCT" expHeader = "chunk1" obsHeader = bioseq.getHeaderFullSeq() self.assertEquals( expHeader, obsHeader ) def test_getFragStrand_plus_strand(self): bioseq = Bioseq() bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74091..74624" bioseq.sequence = "TAATTCGGCCT" expStrand = '+' obsStrand = bioseq.getFragStrand() self.assertEquals(expStrand, obsStrand) def test_getFragStrand_minus_strand(self): bioseq = Bioseq() bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74624..74091" bioseq.sequence = "TAATTCGGCCT" expStrand = '-' obsStrand = bioseq.getFragStrand() self.assertEquals(expStrand, obsStrand) def test_getATGCNFromIUPAC_A(self): bioseq = Bioseq() expNucl = 'A' obsNucl = bioseq.getATGCNFromIUPAC('A') self.assertEquals(expNucl, obsNucl) def test_getATGCNFromIUPAC_T(self): bioseq = Bioseq() expNucl = 'T' obsNucl = bioseq.getATGCNFromIUPAC('T') self.assertEquals(expNucl, obsNucl) def test_getATGCNFromIUPAC_C(self): bioseq = Bioseq() expNucl = 'C' obsNucl = bioseq.getATGCNFromIUPAC('C') self.assertEquals(expNucl, obsNucl) def test_getATGCNFromIUPAC_G(self): bioseq = Bioseq() expNucl = 'G' obsNucl = bioseq.getATGCNFromIUPAC('G') self.assertEquals(expNucl, obsNucl) def test_getATGCNFromIUPAC_N(self): bioseq = Bioseq() expNucl = 'N' obsNucl = bioseq.getATGCNFromIUPAC('N') self.assertEquals(expNucl, obsNucl) def test_getATGCNFromIUPAC_U(self): bioseq = Bioseq() expNucl = 'T' obsNucl = bioseq.getATGCNFromIUPAC('U') self.assertEquals(expNucl, obsNucl) def test_getATGCNFromIUPAC_R(self): bioseq = Bioseq() expNucl1 = 'A' expNucl2 = 'G' obsNucl = bioseq.getATGCNFromIUPAC('R') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) def test_getATGCNFromIUPAC_Y(self): bioseq = Bioseq() expNucl1 = 'C' expNucl2 = 'T' obsNucl = bioseq.getATGCNFromIUPAC('Y') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) def test_getATGCNFromIUPAC_M(self): bioseq = Bioseq() expNucl1 = 'C' expNucl2 = 'A' obsNucl = bioseq.getATGCNFromIUPAC('M') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) def test_getATGCNFromIUPAC_K(self): bioseq = Bioseq() expNucl1 = 'T' expNucl2 = 'G' obsNucl = bioseq.getATGCNFromIUPAC('K') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) def test_getATGCNFromIUPAC_W(self): bioseq = Bioseq() expNucl1 = 'T' expNucl2 = 'A' obsNucl = bioseq.getATGCNFromIUPAC('W') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) def test_getATGCNFromIUPAC_S(self): bioseq = Bioseq() expNucl1 = 'C' expNucl2 = 'G' obsNucl = bioseq.getATGCNFromIUPAC('S') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) def test_getATGCNFromIUPAC_B(self): bioseq = Bioseq() expNucl1 = 'C' expNucl2 = 'T' expNucl3 = 'G' obsNucl = bioseq.getATGCNFromIUPAC('B') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl or expNucl3 == obsNucl) def test_getATGCNFromIUPAC_D(self): bioseq = Bioseq() expNucl1 = 'A' expNucl2 = 'T' expNucl3 = 'G' obsNucl = bioseq.getATGCNFromIUPAC('D') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl or expNucl3 == obsNucl) def test_getATGCNFromIUPAC_H(self): bioseq = Bioseq() expNucl1 = 'C' expNucl2 = 'T' expNucl3 = 'A' obsNucl = bioseq.getATGCNFromIUPAC('H') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl or expNucl3 == obsNucl) def test_getATGCNFromIUPAC_V(self): bioseq = Bioseq() expNucl1 = 'C' expNucl2 = 'A' expNucl3 = 'G' obsNucl = bioseq.getATGCNFromIUPAC('V') self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl or expNucl3 == obsNucl) def test_getATGCNFromIUPAC_Z(self): bioseq = Bioseq() expNucl = 'N' obsNucl = bioseq.getATGCNFromIUPAC('Z') self.assertEquals(expNucl, obsNucl) def test_partialIUPAC(self): bioseq = Bioseq() bioseq.sequence = "ATGCNRATGCN" expSequence1 = "ATGCNAATGCN" expSequence2 = "ATGCNGATGCN" bioseq.partialIUPAC() obsSequence = bioseq.sequence self.assertTrue(expSequence1 == obsSequence or expSequence2 == obsSequence) def test_checkEOF(self): bioseq = Bioseq() bioseq.sequence = "ATGCNRATGCN\rATGCAAT\rTATA\r" bioseq.checkEOF() obsSequence = bioseq.sequence expSequence = "ATGCNRATGCNATGCAATTATA" self.assertEquals(expSequence, obsSequence) def test_getLMapWhithoutGap(self): iBioseq = Bioseq() iBioseq.header = "header" iBioseq.sequence = "ATGC-RA-GCT" obsLMap = iBioseq.getLMapWhithoutGap() expLMap = [Map( "header_subSeq1", "header", 1, 4 ), Map( "header_subSeq2", "header", 6, 7 ), Map( "header_subSeq3", "header", 9, 11 )] self.assertEquals(expLMap, obsLMap) def test_getLMapWhithoutGap_seqStartsWithGap(self): iBioseq = Bioseq() iBioseq.header = "header" iBioseq.sequence = "-TGC-RA-GCT" obsLMap = iBioseq.getLMapWhithoutGap() expLMap = [Map( "header_subSeq1", "header", 2, 4 ), Map( "header_subSeq2", "header", 6, 7 ), Map( "header_subSeq3", "header", 9, 11 )] self.assertEquals(expLMap, obsLMap) def test_getLMapWhithoutGap_seqEndsWithGap(self): iBioseq = Bioseq() iBioseq.header = "header" iBioseq.sequence = "ATGC-RA-GC-" obsLMap = iBioseq.getLMapWhithoutGap() expLMap = [Map( "header_subSeq1", "header", 1, 4 ), Map( "header_subSeq2", "header", 6, 7 ), Map( "header_subSeq3", "header", 9, 10 )] self.assertEquals(expLMap, obsLMap) def test_getGCpercentage_onlyATGC( self ): iBs = Bioseq( "seq", "TGCAGCT" ) exp = 100 * 4 / 7.0 obs = iBs.getGCpercentage() self.assertEqual( exp, obs ) def test_getGCpercentageInSequenceWithoutCountNInLength( self ): iBs = Bioseq( "seq", "TGCAGCTNNNNN" ) exp = 100 * 4 / 7.0 obs = iBs.getGCpercentageInSequenceWithoutCountNInLength() self.assertEqual( exp, obs ) def test_get5PrimeFlank(self): bs = Bioseq( "line1", "AACTTTCCAGAA" ) position = 7 obsFlank = bs.get5PrimeFlank(position, 3) expFlank = "TTT" self.assertEquals(expFlank, obsFlank) def test_get5PrimeFlank_flank_length_truncated(self): bs = Bioseq( "line1", "AACTTTCCAGAA" ) position = 7 obsFlank = bs.get5PrimeFlank(position, 15) expFlank = "AACTTT" self.assertEquals(expFlank, obsFlank) def test_get5PrimeFlank_flank_of_first_base(self): bs = Bioseq( "line1", "AACTTTCCAGAA" ) position = 1 obsFlank = bs.get5PrimeFlank(position, 15) expFlank = "" self.assertEquals(expFlank, obsFlank) def test_get3PrimeFlank(self): bs = Bioseq( "line1", "AACTTTCCAGAA" ) position = 7 obsFlank = bs.get3PrimeFlank(position, 3) expFlank = "CAG" self.assertEquals(expFlank, obsFlank) def test_get3PrimeFlank_flank_length_truncated(self): bs = Bioseq( "line1", "AACTTTCCAGAA" ) position = 7 obsFlank = bs.get3PrimeFlank(position, 15) expFlank = "CAGAA" self.assertEquals(expFlank, obsFlank) def test_get3PrimeFlank_flank_of_last_base(self): bs = Bioseq( "line1", "AACTTTCCAGAA" ) position = 12 obsFlank = bs.get3PrimeFlank(position, 15) expFlank = "" self.assertEquals(expFlank, obsFlank) def test_get3PrimeFlank_polymLength_different_of_1(self): bs = Bioseq( "line1", "AACTTTCCAGAA" ) position = 7 obsFlank = bs.get3PrimeFlank(position, 3, 2) expFlank = "AGA" self.assertEquals(expFlank, obsFlank) test_suite = unittest.TestSuite() test_suite.addTest( unittest.makeSuite( Test_Bioseq ) ) if __name__ == "__main__": unittest.TextTestRunner(verbosity=2).run( test_suite )