Python SamtoolsMpileupCommandline Examples

Example #1

File: test_samtools_tool.py Project: MCalvi/biopython

 def test_mpileup_list(self):
     cmdline = SamtoolsMpileupCommandline(samtools_exe)
     cmdline.set_parameter("input_file", [self.bamfile1, self.bamfile2])
     stdout, stderr = cmdline()
     self.assertFalse("[bam_pileup_core]" in stdout)

Example #2

File: test_samtools_tool.py Project: kctsai066/hello-world

 def test_mpileup_list(self):
     cmdline = SamtoolsMpileupCommandline(samtools_exe)
     cmdline.set_parameter("input_file",
                           [self.sortedbamfile1, self.sortedbamfile2])
     stdout, stderr = cmdline()
     self.assertFalse("[bam_pileup_core]" in stdout)

Example #3

File: test_samtools_tool.py Project: iriziotis/biopython_bugfixes

 def test_mpileup(self):
     cmdline = SamtoolsMpileupCommandline(samtools_exe)
     cmdline.set_parameter("input_file", [self.bamfile1])
     stdout, stderr = cmdline()
     self.assertNotIn("[bam_pileup_core]", stdout)