def runFastqScreen(infiles, outfile):
'''run FastqScreen on input files.'''
# variables required for statement built by FastqScreen()
tempdir = P.getTempDir(".")
outdir = os.path.join(PARAMS["exportdir"], "fastq_screen")
# configure job_threads with fastq_screen_options from PARAMS
job_threads = re.findall(r'--threads \d+', PARAMS['fastq_screen_options'])
if len(job_threads) != 1:
raise ValueError("Wrong number of threads for fastq_screen")
job_threads = int(re.sub(r'--threads ', '', job_threads[0]))
job_memory = "8G"
# Create fastq_screen config file in temp directory
# using parameters from Pipeline.ini
with IOTools.openFile(os.path.join(tempdir, "fastq_screen.conf"),
"w") as f:
for i, k in list(PARAMS.items()):
if i.startswith("fastq_screen_database"):
f.write("DATABASE\t%s\t%s\n" % (i[22:], k))
m = PipelineMapping.FastqScreen()
statement = m.build((infiles,), outfile)
P.run()
shutil.rmtree(tempdir)
P.touch(outfile)
def runFastqScreen(infiles, outfile):
'''run FastqScreen on input files.'''
# variables required for statement built by FastqScreen()
tempdir = P.getTempDir(".")
outdir = os.path.join(PARAMS["exportdir"], "fastq_screen")
# Create fastq_screen config file in temp directory
# using parameters from Pipeline.ini
with IOTools.openFile(os.path.join(tempdir, "fastq_screen.conf"),
"w") as f:
for i, k in PARAMS.items():
if i.startswith("fastq_screen_database"):
f.write("DATABASE\t%s\t%s\n" % (i[22:], k))
m = PipelineMapping.FastqScreen()
statement = m.build((infiles,), outfile)
P.run()
shutil.rmtree(tempdir)
P.touch(outfile)
def runFastqScreen(infiles, outfile):
'''run FastqScreen on input files.'''
# configure job_threads with fastq_screen_options from PARAMS
job_threads = re.findall(r'--threads \d+', PARAMS['fastq_screen_options'])
if len(job_threads) != 1:
raise ValueError("Wrong number of threads for fastq_screen")
job_threads = int(re.sub(r'--threads ', '', job_threads[0]))
tempdir = P.get_temp_dir(".")
conf_fn = os.path.join(tempdir, "fastq_screen.conf")
with IOTools.open_file(conf_fn, "w") as f:
for i, k in PARAMS.items():
if i.startswith("fastq_screen_database"):
f.write("DATABASE\t%s\t%s\n" % (i[22:], k))
m = PipelineMapping.FastqScreen(config_filename=conf_fn)
statement = m.build((infiles,), outfile)
P.run(statement, job_memory="8G")
shutil.rmtree(tempdir)
IOTools.touch_file(outfile)