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src/b/i/biopython-HEAD/Tests/test_samtools_tool.py   biopython(Download)
from Bio.Sequencing.Applications import SamtoolsCalmdCommandline
from Bio.Sequencing.Applications import SamtoolsCatCommandline
from Bio.Sequencing.Applications import SamtoolsFaidxCommandline
from Bio.Sequencing.Applications import SamtoolsIdxstatsCommandline
from Bio.Sequencing.Applications import SamtoolsIndexCommandline
    def create_fasta_index(self):
        """Creates index for reference fasta sequence."""
        cmdline = SamtoolsFaidxCommandline(samtools_exe)
        cmdline.set_parameter("reference", self.reference)
        stdout, stderr = cmdline()
    def test_faidx(self):
        cmdline = SamtoolsFaidxCommandline(samtools_exe)
        cmdline.set_parameter("reference", self.reference)
        stdout, stderr = cmdline()
        self.assertFalse(stderr,