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src/b/i/biopython-HEAD/Tests/test_samtools_tool.py   biopython(Download)
import os
import unittest
from Bio.Sequencing.Applications import SamtoolsViewCommandline
from Bio.Sequencing.Applications import SamtoolsCalmdCommandline
from Bio.Sequencing.Applications import SamtoolsCatCommandline
    def test_view(self):
        """Test for samtools view"""
 
        cmdline = SamtoolsViewCommandline(samtools_exe)
        cmdline.set_parameter("input_file", self.bamfile1)
        stdout_bam, stderr_bam = cmdline()
        cmdline.set_parameter("input_file", self.samfile1)
        cmdline.set_parameter("S", True)
        stdout_sam, stderr_sam = cmdline()
        self.assertTrue(
            stderr_sam.startswith("[samopen] SAM header is present:"),