def test_sort(self):
cmdline = SamtoolsSortCommandline(samtools_exe)
cmdline.set_parameter("input_bam", self.bamfile1)
cmdline.set_parameter("out_prefix", "SamBam/out")
stdout, stderr = cmdline()
self.assertFalse(
stderr, "Samtools sort failed:\n%s\nStderr:%s" % (cmdline, stderr))
def test_sort(self):
cmdline = SamtoolsSortCommandline(samtools_exe)
cmdline.set_parameter("input_bam", self.bamfile1)
cmdline.set_parameter("out_prefix", "bam1")
stdout, stderr = cmdline()
self.assertFalse(stderr,
"Samtools sort failed:\n%s\nStderr:%s"
% (cmdline, stderr))
def test_sort(self):
cmdline = SamtoolsSortCommandline(samtools_exe)
cmdline.set_parameter("input_bam", self.bamfile1)
cmdline.set_parameter("out_prefix", "SamBam/out")
try:
stdout, stderr = cmdline()
except ApplicationError as err:
if "[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files" in str(err):
# TODO: The samtools sort API changed...
return
else:
raise
self.assertFalse(stderr,
"Samtools sort failed:\n%s\nStderr:%s"
% (cmdline, stderr))
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