Python parseBed Examples

Example #1

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalCompleteNoStrand(self):
        self.row[5] = '.'  # change strand
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(7, len(transcript.exons))

        for start, end, seqType in transcript.exons:
            self.assertEqual('exon', seqType)

Example #2

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalCompleteNoStrand(self):
        self.row[5] = '.'  # change strand
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(7, len(transcript.exons))

        for start, end, seqType in transcript.exons:
            self.assertEqual('exon', seqType)

Example #3

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalPositiveStrandNo_5_UTR(self):
        self.row[6] = 80303035  # change thickStart
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(10, len(transcript.exons))

        self.assertEqual((80303036, 80303038, 'start_codon'), transcript.exons[0])

        for start, end, seqType in transcript.exons[1:-2]:
            self.assertEqual(seqType, 'CDS')

Example #4

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalPositiveStrandNo_3_UTR(self):
        self.row[7] = 80306166  # change thickStart
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(10, len(transcript.exons))

        self.assertEqual((80306164, 80306166, 'stop_codon'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[2:-1]:
            self.assertEqual(seqType, 'CDS')

Example #5

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalPositiveStrandNo_3_UTR(self):
        self.row[7] = 80306166  # change thickStart
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(10, len(transcript.exons))

        self.assertEqual((80306164, 80306166, 'stop_codon'),
                         transcript.exons[-1])

        for start, end, seqType in transcript.exons[2:-1]:
            self.assertEqual(seqType, 'CDS')

Example #6

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalNegativeStrandShort_5_3_UTR(self):
        self.row[5] = '-'
        self.row[6] = 80303036  # change thickStart
        self.row[7] = 80306165  # change thickEnd

        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303036,'3UTR'), transcript.exons[0])
        self.assertEqual((80306166, 80306166,'5UTR'), transcript.exons[-1])

Example #7

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalNegativeStrandNo_5_UTR(self):
        self.row[5] = '-'  # change strand
        self.row[7] = 80306166
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(10, len(transcript.exons))

        self.assertEqual((80306164, 80306166, 'start_codon'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[2:-1]:
            self.assertEqual(seqType, 'CDS')

Example #8

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalPositiveStrandNo_5_UTR(self):
        self.row[6] = 80303035  # change thickStart
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(10, len(transcript.exons))

        self.assertEqual((80303036, 80303038, 'start_codon'),
                         transcript.exons[0])

        for start, end, seqType in transcript.exons[1:-2]:
            self.assertEqual(seqType, 'CDS')

Example #9

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalCompletePositiveStrand(self):
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(transcript.chromosome, 'chr1')
        self.assertEqual(transcript.chromStart, 80303035)
        self.assertEqual(transcript.chromEnd, 80306166)
        self.assertEqual(transcript.strand, '+')
        self.assertEqual(transcript.transcriptName, '1')
        self.assertEqual(transcript.geneName, '8')
        self.assertEqual(transcript.exonStarts, [0, 352, 879, 1043, 1705, 2090, 2521])
        self.assertEqual(transcript.exonSizes, [260, 76, 89, 203, 106, 152, 610])

Example #10

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalNegativeStrandShort_5_3_UTR(self):
        self.row[5] = '-'
        self.row[6] = 80303036  # change thickStart
        self.row[7] = 80306165  # change thickEnd

        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303036, '3UTR'), transcript.exons[0])
        self.assertEqual((80306166, 80306166, '5UTR'), transcript.exons[-1])

Example #11

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalNegativeStrandNo_5_UTR(self):
        self.row[5] = '-'  # change strand
        self.row[7] = 80306166
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(10, len(transcript.exons))

        self.assertEqual((80306164, 80306166, 'start_codon'),
                         transcript.exons[-1])

        for start, end, seqType in transcript.exons[2:-1]:
            self.assertEqual(seqType, 'CDS')

Example #12

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalCompletePositiveStrand(self):
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(transcript.chromosome, 'chr1')
        self.assertEqual(transcript.chromStart, 80303035)
        self.assertEqual(transcript.chromEnd, 80306166)
        self.assertEqual(transcript.strand, '+')
        self.assertEqual(transcript.transcriptName, '1')
        self.assertEqual(transcript.geneName, '8')
        self.assertEqual(transcript.exonStarts,
                         [0, 352, 879, 1043, 1705, 2090, 2521])
        self.assertEqual(transcript.exonSizes,
                         [260, 76, 89, 203, 106, 152, 610])

Example #13

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalNegativeStrandNo_3_UTR(self):
        self.row[5] = '-'  # change strand
        self.row[6] = 80303035
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(10, len(transcript.exons))

        self.assertEqual((80303036, 80303038, 'stop_codon'), transcript.exons[0])
        self.assertEqual((80305594, 80305596, 'start_codon'), transcript.exons[-2])
        self.assertEqual((80305597, 80306166,'5UTR'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[1:-2]:
            self.assertEqual(seqType, 'CDS')

Example #14

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalNegativeStrandNo_5_3_UTR(self):
        self.row[5] = '-'  # change strand
        self.row[6] = 80303035  # change thickStart
        self.row[7] = 80306166  # change thickEnd

        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(9, len(transcript.exons))

        self.assertEqual((80303036, 80303038, 'stop_codon'), transcript.exons[0])
        self.assertEqual((80306164, 80306166, 'start_codon'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[1:-1]:
            self.assertEqual(seqType, 'CDS')

Example #15

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesSplitStopCodonPositiveStrand(self):
        self.row[7] = 80305557
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303046, '5UTR'), transcript.exons[0])
        self.assertEqual((80303047, 80303049, 'start_codon'), transcript.exons[1])
        self.assertEqual((80305276, 80305277, 'stop_codon'), transcript.exons[-3])
        self.assertEqual((80305557, 80305557, 'stop_codon'), transcript.exons[-2])
        self.assertEqual((80305558, 80306166, '3UTR'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[2:-3]:
            self.assertEqual(seqType, 'CDS')

Example #16

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalPositiveStrandShort_5_3_UTR(self):
        self.row[6] = 80303036  # change thickStart
        self.row[7] = 80306165  # change thickEnd

        transcript = bed2gff.parseBed(self.row)
        '''
        print >> sys.stderr, '\n'
        for i in range(len(transcript.exons)):
            print >> sys.stderr, i + 1, transcript.exons[i]
        '''

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303036, '5UTR'), transcript.exons[0])
        self.assertEqual((80306166, 80306166, '3UTR'), transcript.exons[-1])

Example #17

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalCompleteNegativeStrand(self):
        self.row[5] = '-'  # change strand
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303046, '3UTR'), transcript.exons[0])
        self.assertEqual((80303047, 80303049, 'stop_codon'), transcript.exons[1])
        self.assertEqual((80303050, 80303295, 'CDS'), transcript.exons[2])
        self.assertEqual((80305557, 80305596, 'CDS'), transcript.exons[-3])
        self.assertEqual((80305594, 80305596, 'start_codon'), transcript.exons[-2])
        self.assertEqual((80305597, 80306166,'5UTR'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[2:-2]:
            self.assertEqual(seqType, 'CDS')

Example #18

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalNegativeStrandNo_3_UTR(self):
        self.row[5] = '-'  # change strand
        self.row[6] = 80303035
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(10, len(transcript.exons))

        self.assertEqual((80303036, 80303038, 'stop_codon'),
                         transcript.exons[0])
        self.assertEqual((80305594, 80305596, 'start_codon'),
                         transcript.exons[-2])
        self.assertEqual((80305597, 80306166, '5UTR'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[1:-2]:
            self.assertEqual(seqType, 'CDS')

Example #19

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalCompletePositiveStrand(self):
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        print >> sys.stderr, '\n'
        for i in range(len(transcript.exons)):
            print >> sys.stderr, i + 1, transcript.exons[i]

        self.assertEqual((80303036, 80303046, '5UTR'), transcript.exons[0])
        self.assertEqual((80303047, 80303049, 'start_codon'), transcript.exons[1])
        self.assertEqual((80303047, 80303295, 'CDS'), transcript.exons[2])
        self.assertEqual((80305594, 80305596, 'stop_codon'), transcript.exons[-2])

        for start, end, seqType in transcript.exons[2:-2]:
            self.assertEqual(seqType, 'CDS')

Example #20

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalPositiveStrandShort_5_3_UTR(self):
        self.row[6] = 80303036  # change thickStart
        self.row[7] = 80306165  # change thickEnd

        transcript = bed2gff.parseBed(self.row)

        '''
        print >> sys.stderr, '\n'
        for i in range(len(transcript.exons)):
            print >> sys.stderr, i + 1, transcript.exons[i]
        '''

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303036,'5UTR'), transcript.exons[0])
        self.assertEqual((80306166, 80306166,'3UTR'), transcript.exons[-1])

Example #21

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalNegativeStrandNo_5_3_UTR(self):
        self.row[5] = '-'  # change strand
        self.row[6] = 80303035  # change thickStart
        self.row[7] = 80306166  # change thickEnd

        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(9, len(transcript.exons))

        self.assertEqual((80303036, 80303038, 'stop_codon'),
                         transcript.exons[0])
        self.assertEqual((80306164, 80306166, 'start_codon'),
                         transcript.exons[-1])

        for start, end, seqType in transcript.exons[1:-1]:
            self.assertEqual(seqType, 'CDS')

Example #22

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesSplitStopCodonPositiveStrand(self):
        self.row[7] = 80305557
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303046, '5UTR'), transcript.exons[0])
        self.assertEqual((80303047, 80303049, 'start_codon'),
                         transcript.exons[1])
        self.assertEqual((80305276, 80305277, 'stop_codon'),
                         transcript.exons[-3])
        self.assertEqual((80305557, 80305557, 'stop_codon'),
                         transcript.exons[-2])
        self.assertEqual((80305558, 80306166, '3UTR'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[2:-3]:
            self.assertEqual(seqType, 'CDS')

Example #23

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalCompleteNegativeStrand(self):
        self.row[5] = '-'  # change strand
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303046, '3UTR'), transcript.exons[0])
        self.assertEqual((80303047, 80303049, 'stop_codon'),
                         transcript.exons[1])
        self.assertEqual((80303050, 80303295, 'CDS'), transcript.exons[2])
        self.assertEqual((80305557, 80305596, 'CDS'), transcript.exons[-3])
        self.assertEqual((80305594, 80305596, 'start_codon'),
                         transcript.exons[-2])
        self.assertEqual((80305597, 80306166, '5UTR'), transcript.exons[-1])

        for start, end, seqType in transcript.exons[2:-2]:
            self.assertEqual(seqType, 'CDS')

Example #24

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesNormalCompletePositiveStrand(self):
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        print >> sys.stderr, '\n'
        for i in range(len(transcript.exons)):
            print >> sys.stderr, i + 1, transcript.exons[i]

        self.assertEqual((80303036, 80303046, '5UTR'), transcript.exons[0])
        self.assertEqual((80303047, 80303049, 'start_codon'),
                         transcript.exons[1])
        self.assertEqual((80303047, 80303295, 'CDS'), transcript.exons[2])
        self.assertEqual((80305594, 80305596, 'stop_codon'),
                         transcript.exons[-2])

        for start, end, seqType in transcript.exons[2:-2]:
            self.assertEqual(seqType, 'CDS')

Example #25

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesSplitStartCodonPositiveStrand(self):
        self.row[6] = 80303293  # change thickStart
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(12, len(transcript.exons))

        self.assertEqual((80303036, 80303293, '5UTR'), transcript.exons[0])
        self.assertEqual((80303294, 80303295, 'start_codon'), transcript.exons[1])
        self.assertEqual((80303294, 80303295, 'CDS'), transcript.exons[2])
        self.assertEqual((80303388, 80303388, 'start_codon'), transcript.exons[3])
        self.assertEqual((80303388, 80303463, 'CDS'), transcript.exons[4])


        for start, end, seqType in transcript.exons[4:-2]:
            self.assertEqual(seqType, 'CDS')

        self.assertEqual('stop_codon', transcript.exons[-2][-1])
        self.assertEqual('3UTR', transcript.exons[-1][-1])

Example #26

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

    def testTranscriptFeaturesSplitStopCodonNegativeStrand(self):
        self.row[6] = 80303293  # modifythickStart
        self.row[5] = '-'  # modify strand
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303293, '3UTR'), transcript.exons[0])
        self.assertEqual((80303294, 80303295, 'stop_codon'), transcript.exons[1])
        self.assertEqual((80303388, 80303388, 'stop_codon'), transcript.exons[2])
        self.assertEqual((80303389, 80303463, 'CDS'), transcript.exons[3])


        for start, end, seqType in transcript.exons[3:-2]:
            self.assertEqual(seqType, 'CDS')

        self.assertEqual('start_codon', transcript.exons[-2][-1])
        self.assertEqual('5UTR', transcript.exons[-1][-1])

Example #27

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesSplitStartCodonPositiveStrand(self):
        self.row[6] = 80303293  # change thickStart
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(12, len(transcript.exons))

        self.assertEqual((80303036, 80303293, '5UTR'), transcript.exons[0])
        self.assertEqual((80303294, 80303295, 'start_codon'),
                         transcript.exons[1])
        self.assertEqual((80303294, 80303295, 'CDS'), transcript.exons[2])
        self.assertEqual((80303388, 80303388, 'start_codon'),
                         transcript.exons[3])
        self.assertEqual((80303388, 80303463, 'CDS'), transcript.exons[4])

        for start, end, seqType in transcript.exons[4:-2]:
            self.assertEqual(seqType, 'CDS')

        self.assertEqual('stop_codon', transcript.exons[-2][-1])
        self.assertEqual('3UTR', transcript.exons[-1][-1])

Example #28

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

    def testTranscriptFeaturesSplitStopCodonNegativeStrand(self):
        self.row[6] = 80303293  # modifythickStart
        self.row[5] = '-'  # modify strand
        transcript = bed2gff.parseBed(self.row)

        self.assertEqual(11, len(transcript.exons))

        self.assertEqual((80303036, 80303293, '3UTR'), transcript.exons[0])
        self.assertEqual((80303294, 80303295, 'stop_codon'),
                         transcript.exons[1])
        self.assertEqual((80303388, 80303388, 'stop_codon'),
                         transcript.exons[2])
        self.assertEqual((80303389, 80303463, 'CDS'), transcript.exons[3])

        for start, end, seqType in transcript.exons[3:-2]:
            self.assertEqual(seqType, 'CDS')

        self.assertEqual('start_codon', transcript.exons[-2][-1])
        self.assertEqual('5UTR', transcript.exons[-1][-1])

Example #29

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

 def testNormalThickEnd(self):
     transcript = bed2gff.parseBed(self.row)
     self.assertEqual(80305594, transcript._newThickEnd())

Example #30

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

 def testSplitThickEnd4(self):
     self.row[7] = 80305559
     transcript = bed2gff.parseBed(self.row)
     self.assertEqual(80305557, transcript._newThickEnd())

Example #31

File: testbed2gff.py Project: icefoxx/python-codes-for-RNAseq

 def testNormalThickEnd(self):
     transcript = bed2gff.parseBed(self.row)
     self.assertEqual(80305594, transcript._newThickEnd())

Example #32

File: testbed2gff.py Project: bjventers/python-codes-for-RNAseq

 def testSplitThickEnd4(self):
     self.row[7] = 80305559
     transcript = bed2gff.parseBed(self.row)
     self.assertEqual(80305557, transcript._newThickEnd())