Example #1
0
    def test_parse(self):
        for label, seq, qual in parse_fastq(self.FASTQ_EXAMPLE, phred_offset=64):
            self.assertTrue(label in DATA)
            self.assertEqual(seq, DATA[label]["seq"])
            self.assertTrue((qual == DATA[label]["qual"]).all())

        # Make sure that enforce_qual_range set to False allows qual scores
        # to fall outside the typically acceptable range of 0-62
        for label, seq, qual in parse_fastq(self.FASTQ_EXAMPLE_2, phred_offset=33, enforce_qual_range=False):
            self.assertTrue(label in DATA_2)
            self.assertEqual(seq, DATA_2[label]["seq"])
            self.assertTrue((qual == DATA_2[label]["qual"]).all())

        # This should raise a FastqParseError since the qual scores are
        # intended to be interpreted with an offset of 64, and using 33 will
        # make the qual score fall outside the acceptable range of 0-62.
        with self.assertRaises(FastqParseError):
            list(parse_fastq(self.FASTQ_EXAMPLE, phred_offset=33))
Example #2
0
    def test_parse(self):
        for label, seq, qual in parse_fastq(self.FASTQ_EXAMPLE,
                                            phred_offset=64):
            self.assertTrue(label in DATA)
            self.assertEqual(seq, DATA[label]["seq"])
            self.assertTrue((qual == DATA[label]["qual"]).all())

        # Make sure that enforce_qual_range set to False allows qual scores
        # to fall outside the typically acceptable range of 0-62
        for label, seq, qual in parse_fastq(self.FASTQ_EXAMPLE_2,
                                            phred_offset=33,
                                            enforce_qual_range=False):
            self.assertTrue(label in DATA_2)
            self.assertEqual(seq, DATA_2[label]["seq"])
            self.assertTrue((qual == DATA_2[label]["qual"]).all())

        # This should raise a FastqParseError since the qual scores are
        # intended to be interpreted with an offset of 64, and using 33 will
        # make the qual score fall outside the acceptable range of 0-62.
        with self.assertRaises(FastqParseError):
            list(parse_fastq(self.FASTQ_EXAMPLE, phred_offset=33))
Example #3
0
 def test_invalid_phred_offset(self):
     with self.assertRaises(ValueError):
         list(parse_fastq(self.FASTQ_EXAMPLE, phred_offset=42))
Example #4
0
    def test_parse_error(self):
        with self.assertRaises(FastqParseError):
            list(parse_fastq(self.FASTQ_EXAMPLE_2, strict=True))

        with self.assertRaises(FastqParseError):
            list(parse_fastq(self.FASTQ_EXAMPLE_3, phred_offset=64))
Example #5
0
 def test_invalid_phred_offset(self):
     with self.assertRaises(ValueError):
         list(parse_fastq(self.FASTQ_EXAMPLE, phred_offset=42))
Example #6
0
    def test_parse_error(self):
        with self.assertRaises(FastqParseError):
            list(parse_fastq(self.FASTQ_EXAMPLE_2, strict=True))

        with self.assertRaises(FastqParseError):
            list(parse_fastq(self.FASTQ_EXAMPLE_3, phred_offset=64))