def test_bowtie2_align(variables):
outpath = os.path.join(variables.path, 'bait')
outfile = os.path.join(outpath, 'map_test_sorted.bam')
targetpath = os.path.join(variables.targetpath, 'bait')
# Use samtools wrapper to set up the bam sorting command
samsort = SamtoolsSortCommandline(input=outfile, o=True, out_prefix="-")
samtools = [
# When bowtie2 maps reads to all possible locations rather than choosing a 'best' placement, the
# SAM header for that read is set to 'secondary alignment', or 256. Please see:
# http://davetang.org/muse/2014/03/06/understanding-bam-flags/ The script below reads in the stdin
# and subtracts 256 from headers which include 256
'python3 {}'.format(scriptpath),
# Use samtools wrapper to set up the samtools view
SamtoolsViewCommandline(b=True, S=True, h=True, input_file="-"),
samsort
]
# Add custom parameters to a dictionary to be used in the bowtie2 alignment wrapper
indict = {
'--very-sensitive-local': True,
'-U': os.path.join(targetpath, 'genesippr.fastq.gz'),
'-a': True,
'--threads': multiprocessing.cpu_count(),
'--local': True
}
# Create the bowtie2 reference mapping command
bowtie2align = Bowtie2CommandLine(bt2=os.path.join(targetpath,
'baitedtargets'),
threads=multiprocessing.cpu_count(),
samtools=samtools,
**indict)
bowtie2align(cwd=outpath)
size = os.stat(outfile)
assert size.st_size > 0
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))