def runFastQC(infiles, outfile):
'''run FastQC on each input file.
convert sra files to fastq and check mapping qualities are in
solexa format. Perform quality control checks on reads from
.fastq files.
'''
# only pass the contaminants file list if requested by user,
if PARAMS['use_custom_contaminants']:
m = PipelineMapping.FastQC(nogroup=PARAMS["readqc_no_group"],
outdir=os.path.dirname(outfile),
contaminants=PARAMS['contaminants_path'],
qual_format=PARAMS['qual_format'])
else:
m = PipelineMapping.FastQC(nogroup=PARAMS["readqc_no_group"],
outdir=os.path.dirname(outfile),
qual_format=PARAMS['qual_format'])
if PARAMS["reconcile"] == 1:
infiles = infiles.replace("processed.dir/trimmed",
"reconciled.dir/trimmed")
statement = m.build((infiles,), outfile)
P.run(statement)
def runFastQC(infiles, outfile):
'''run FastQC on each input file.
check mapping qualities are in solexa format for downloaded .fastq
and .bam files. Perform quality control checks on reads from
.fastq and .bam files.
'''
infile = infiles
outdir = os.path.dirname(outfile)
if infile.endswith(".bam"):
statement = '''fastqc --extract --outdir=%(outdir)s %(infile)s >& %(outfile)s'''
else:
# outfile = os.path.join(outdir, os.path.basename(outfile.split(os.extsep, 2)[1] + ".fastqc"))
m = PipelineMapping.FastQC(nogroup=PARAMS["readqc_no_group"],
outdir=outdir,
qual_format=PARAMS['readqc_qual_format'])
statement = m.build((infile, ), outfile)
if not os.path.isfile(outfile):
P.run(statement)
else:
pass