def test_view(self):
"""Test for samtools view."""
cmdline = SamtoolsViewCommandline(samtools_exe)
cmdline.set_parameter("input_file", self.bamfile1)
stdout_bam, stderr_bam = cmdline()
self.assertTrue(
stderr_bam.startswith(""),
"SAM file viewing failed: \n%s\nStdout:%s" % (cmdline, stdout_bam))
cmdline.set_parameter("input_file", self.samfile1)
cmdline.set_parameter("S", True)
stdout_sam, stderr_sam = cmdline()
self.assertTrue(
stdout_sam.startswith("HWI-1KL120:88:D0LRBACXX:1:1101:1780:2146"),
"SAM file viewing failed:\n%s\nStderr:%s" % (cmdline, stderr_sam))
def test_view(self):
"""Test for samtools view"""
cmdline = SamtoolsViewCommandline(samtools_exe)
cmdline.set_parameter("input_file", self.bamfile1)
stdout_bam, stderr_bam = cmdline()
self.assertTrue(stderr_bam.startswith(""), "SAM file viewing failed: \n%s\nStdout:%s" % (cmdline, stdout_bam))
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:"),
"SAM file viewing failed:\n%s\nStderr:%s" % (cmdline, stderr_sam),
)
def test_view(self):
"""Test for samtools view"""
cmdline = SamtoolsViewCommandline(samtools_exe)
cmdline.set_parameter("input_file", self.bamfile1)
stdout_bam, stderr_bam = cmdline()
self.assertTrue(
stderr_bam.startswith(""),
"SAM file viewing failed: \n%s\nStdout:%s" % (cmdline, stdout_bam))
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:"),
"SAM file viewing failed:\n%s\nStderr:%s" % (cmdline, stderr_sam))
def test_view(self):
"""Test for samtools view."""
cmdline = SamtoolsViewCommandline(samtools_exe)
cmdline.set_parameter("input_file", self.bamfile1)
stdout_bam, stderr_bam = cmdline()
self.assertTrue(stderr_bam.startswith(""),
"SAM file viewing failed: \n%s\nStdout:%s"
% (cmdline, stdout_bam))
cmdline.set_parameter("input_file", self.samfile1)
cmdline.set_parameter("S", True)
stdout_sam, stderr_sam = cmdline()
self.assertTrue(
stdout_sam.startswith("HWI-1KL120:88:D0LRBACXX:1:1101:1780:2146"),
"SAM file viewing failed:\n%s\nStderr:%s"
% (cmdline, stderr_sam))
