Python write_rows Exemples

Exemple #1

    def testMinCount(self):
        counts = [
            (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
              "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
              "TGTACAAGA-------------------------------------------------"
              "--------------------------------------------------"), 3),
            (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
              "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
              "TGTACAGGG-------------------------------------------------"
              "--------------------------------------------------"), 2),
            (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
              "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
              "TGTACAGAA-------------------------------------------------"
              "--------------------------------------------------"), 2)
        ]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,3,,,,CTR,,cysteines,
2,4,,,,,,count < 3,
"""
        expected_summary_csv = """\
mapped,valid,X4calls,X4pct,final,validpct
7,0,0,,,0.00
"""

        write_rows(self.pssm,
                   counts,
                   self.g2p_csv,
                   self.g2p_summary_csv,
                   min_count=3)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())
        self.assertEqual(expected_summary_csv, self.g2p_summary_csv.getvalue())

Exemple #2

    def testSummaryX4(self):
        counts = [
            (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
              "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
              "TGTATGAGACCCAACAACAATACAAGAAAAAGTATACATAT------AGGACCAGGGA"
              "GAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACGAGCACATTGT"), 2),
            (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
              "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
              "TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATAT------AGGACCAGGGA"
              "GAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT"), 1)
        ]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,2,0.454349,2.6,X4,CMRPNNNTRKSIHIGPGRAFYATGEIIGDIRRAHC,CMRPN-NNT--RKSIHI---GPGR---AFYAT----GEIIGDI--RRAHC,,
2,1,0.067754,42.3,R5,CTRPNNNTRKSIHIGPGRAFYATGEIIGDIRQAHC,CTRPN-NNT--RKSIHI---GPGR---AFYAT----GEIIGDI--RQAHC,,
"""
        expected_summary_csv = """\
mapped,valid,X4calls,X4pct,final,validpct
3,3,2,66.67,X4,100.00
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())
        self.assertEqual(expected_summary_csv, self.g2p_summary_csv.getvalue())

Exemple #3

Fichier : test_fastq_g2p.py Projet : cfe-lab/MiCall

    def testSummaryX4(self):
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTATGAGACCCAACAACAATACAAGAAAAAGTATACATAT------AGGACCAGGGA"
                    "GAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACGAGCACATTGT"),
                   2),
                  (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATAT------AGGACCAGGGA"
                    "GAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,2,0.454349,2.6,X4,CMRPNNNTRKSIHIGPGRAFYATGEIIGDIRRAHC,CMRPN-NNT--RKSIHI---GPGR---AFYAT----GEIIGDI--RRAHC,,
2,1,0.067754,42.3,R5,CTRPNNNTRKSIHIGPGRAFYATGEIIGDIRQAHC,CTRPN-NNT--RKSIHI---GPGR---AFYAT----GEIIGDI--RQAHC,,
"""
        expected_summary_csv = """\
mapped,valid,X4calls,X4pct,final,validpct
3,3,2,66.67,X4,100.00
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())
        self.assertEqual(expected_summary_csv, self.g2p_summary_csv.getvalue())

Exemple #4

    def testSummaryValidPercentageThresholdFailed(self):
        counts = [
            (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
              "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
              "TGTACAAGACCCAACAACAATACAAGAAAAA------GTATACATATAGGACCAGGGA"
              "GAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT"), 300),
            (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
              "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
              "TGTACAAGA-------------------------------------------------"
              "--------------------------------------------------"), 100)
        ]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,300,0.067754,42.3,R5,CTRPNNNTRKSIHIGPGRAFYATGEIIGDIRQAHC,CTRPN-NNT--RKSIHI---GPGR---AFYAT----GEIIGDI--RQAHC,,
2,100,,,,CTR,,cysteines,
"""
        expected_summary_csv = """\
mapped,valid,X4calls,X4pct,final,validpct
400,300,0,0.00,,75.00
"""

        write_rows(self.pssm,
                   counts,
                   self.g2p_csv,
                   self.g2p_summary_csv,
                   min_valid=300,
                   min_valid_percent=75.1)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())
        self.assertEqual(expected_summary_csv, self.g2p_summary_csv.getvalue())

Exemple #5

Fichier : test_fastq_g2p.py Projet : cfe-lab/MiCall

    def testMinCount(self):
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGA-------------------------------------------------"
                    "--------------------------------------------------"),
                   3),
                  (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAGGG-------------------------------------------------"
                    "--------------------------------------------------"),
                   2),
                  (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAGAA-------------------------------------------------"
                    "--------------------------------------------------"),
                   2)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,3,,,,CTR,,cysteines,
2,4,,,,,,count < 3,
"""
        expected_summary_csv = """\
mapped,valid,X4calls,X4pct,final,validpct
7,0,0,,,0.00
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv, min_count=3)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())
        self.assertEqual(expected_summary_csv, self.g2p_summary_csv.getvalue())

Exemple #6

Fichier : test_fastq_g2p.py Projet : cfe-lab/MiCall

    def testSummaryValidPercentageThresholdFailed(self):
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGACCCAACAACAATACAAGAAAAA------GTATACATATAGGACCAGGGA"
                    "GAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT"),
                   300),
                  (("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGA-------------------------------------------------"
                    "--------------------------------------------------"),
                   100)                  ]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,300,0.067754,42.3,R5,CTRPNNNTRKSIHIGPGRAFYATGEIIGDIRQAHC,CTRPN-NNT--RKSIHI---GPGR---AFYAT----GEIIGDI--RQAHC,,
2,100,,,,CTR,,cysteines,
"""
        expected_summary_csv = """\
mapped,valid,X4calls,X4pct,final,validpct
400,300,0,0.00,,75.00
"""

        write_rows(self.pssm,
                   counts,
                   self.g2p_csv,
                   self.g2p_summary_csv,
                   min_valid=300,
                   min_valid_percent=75.1)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())
        self.assertEqual(expected_summary_csv, self.g2p_summary_csv.getvalue())

Exemple #7

    def testSimple(self):
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGA-------------------------------------------------"
                    "--------------------------------------------------"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,,,,CTR,,cysteines,
"""

        write_rows(self.pssm, counts, self.g2p_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())

Exemple #8

    def testLengthTooShort(self):
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAA-------"
                    "--------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGT"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,,,,CGGGGGGGGGGGGGGGKGGGGGGGGGGGGGC,,length,
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())

Exemple #9

    def testStopCodon(self):
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTTAGTGT-------------------------------------------------"
                    "--------------------------------------------------"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,,,,C*C,,stop codons,
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())

Exemple #10

    def testLowQuality(self):
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TNTNNNGGN-------------------------------------------------"
                    "--------------------------------------------------"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,,,,,,low quality,
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())

Exemple #11

    def testAmbiguousAtTwoPositions(self):
        """ Same thing with codons 9 and 18 - rejected. """
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGACCCAACAACAATACAAGNAAAAG------TATACATATAGGACCAGGGA"
                    "GNGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,,,,CTRPNNNTXKSIHIGPGXAFYATGEIIGDIRQAHC,,> 2 ambiguous,
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())

Exemple #12

    def testAmbiguousMixtureThreeChoices(self):
        """ Marking position 14 as low quality means codon 5 could be L, S, or *.
        """
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGACCCTNAAACTGT-------------------------------------"
                    "--------------------------------------------------"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,,,,CTRPXNC,,> 2 ambiguous,
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())

Exemple #13

    def testAmbiguousMixture(self):
        """ Marking position 9 as low quality means codon 3 could be S or R.
        """
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGNCCCAACAACAATACAAGAAAAAG------TATACATATAGGACCAGGGA"
                    "GAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,0.066305,43.0,R5,CT[RS]PNNNTRKSIHIGPGRAFYATGEIIGDIRQAHC,CT[RS]PN-NNT--RKSIHI---GPGR---AFYAT----GEIIGDI--RQAHC,,ambiguous
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())

Exemple #14

    def testSynonymMixture(self):
        """ Marking position 12 as low quality means codon 4 has to be P.
        """
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTT---GTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGACCNAACAACAATACAAGAAAAAG------TATACATATAGGACCAGGGA"
                    "GAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,0.067754,42.3,R5,CTRPNNNTRKSIHIGPGRAFYATGEIIGDIRQAHC,CTRPN-NNT--RKSIHI---GPGR---AFYAT----GEIIGDI--RQAHC,,
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())

Exemple #15

    def testSummaryFailed(self):
        counts = [(("TGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGA"
                    "GAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGT",
                    "TGTACAAGA-------------------------------------------------"
                    "--------------------------------------------------"),
                   1)]
        expected_g2p_csv = """\
rank,count,g2p,fpr,call,seq,aligned,error,comment
1,1,,,,CTR,,cysteines,
"""
        expected_summary_csv = """\
mapped,valid,X4calls,X4pct,final,validpct
1,0,0,,,0.00
"""

        write_rows(self.pssm, counts, self.g2p_csv, self.g2p_summary_csv)

        self.assertEqual(expected_g2p_csv, self.g2p_csv.getvalue())
        self.assertEqual(expected_summary_csv, self.g2p_summary_csv.getvalue())