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src/b/i/biopython-HEAD/Tests/test_samtools_tool.py   biopython(Download)
from Bio.Sequencing.Applications import SamtoolsIndexCommandline
from Bio.Sequencing.Applications import SamtoolsMergeCommandline
from Bio.Sequencing.Applications import SamtoolsMpileupCommandline
from Bio.Sequencing.Applications import SamtoolsSortCommandline
#TODO from Bio.Sequencing.Applications import SamtoolsPhaseCommandline
    def test_mpileup(self):
        cmdline = SamtoolsMpileupCommandline(samtools_exe)
        cmdline.set_parameter("input_file", [self.bamfile1])
        stdout, stderr = cmdline()
        self.assertFalse("[bam_pileup_core]" in stdout)
 
    def test_mpileup_list(self):
        cmdline = SamtoolsMpileupCommandline(samtools_exe)
        cmdline.set_parameter("input_file", [self.bamfile1, self.bamfile2])
        stdout, stderr = cmdline()