Python rmdup_cdhit_bam Examples

Example #1

File: test_read_utils.py Project: notestaff/viral-ngs

 def test_cdhit_empty_input(self):
     samtools = tools.samtools.SamtoolsTool()
     empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
     output_bam = util.file.mkstempfname("output.bam")
     read_utils.rmdup_cdhit_bam(
         empty_bam,
         output_bam
     )
     self.assertEqual(samtools.count(output_bam), 0)

Example #2

File: test_read_utils.py Project: broadinstitute/viral-ngs

 def test_cdhit_empty_input(self):
     samtools = tools.samtools.SamtoolsTool()
     empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
     output_bam = util.file.mkstempfname("output.bam")
     read_utils.rmdup_cdhit_bam(
         empty_bam,
         output_bam
     )
     self.assertEqual(samtools.count(output_bam), 0)

Example #3

    def test_cdhit_canned_input(self):
        samtools = tools.samtools.SamtoolsTool()

        input_bam = os.path.join(util.file.get_test_input_path(self),
                                 'input.bam')
        expected_bam = os.path.join(util.file.get_test_input_path(self),
                                    'expected.bam')
        output_bam = util.file.mkstempfname("output.bam")
        read_utils.rmdup_cdhit_bam(input_bam, output_bam)

        self.assertEqual(samtools.count(output_bam), 1772)

Example #4

File: test_read_utils.py Project: broadinstitute/viral-ngs

    def test_cdhit_canned_input(self):
        samtools = tools.samtools.SamtoolsTool()

        input_bam = os.path.join(util.file.get_test_input_path(self), 'input.bam')
        expected_bam = os.path.join(util.file.get_test_input_path(self), 'expected.bam')
        output_bam = util.file.mkstempfname("output.bam")
        read_utils.rmdup_cdhit_bam(
            input_bam,
            output_bam
        )

        self.assertEqual(samtools.count(output_bam), 1772)