Commit fc0511f0 authored by Laure QUINTRIC's avatar Laure QUINTRIC

format data for frogs

parent 57cd09f7
......@@ -127,6 +127,10 @@ if __name__ == '__main__':
jobs.append(out.strip().split(".")[0])
logger.debug("job number : {}".format(out))
#create frogs archive
cmd="cd {}/frogs; tar cvf samples.tar *_{{R1,R2}}.fastq.gz && rm {}/frogs/*_{{R1,R2}}.fastq.gz".format(output, output)
out=runcmd(cmd)
#check if number of generated files is ok
cmd="qsub -o {}/logs -V -W depend=afterok:{} {}/check.pbs".format(output,":".join(jobs), directory)
check = runcmd(cmd).strip().split(".")[0]
......
......@@ -223,14 +223,9 @@ if __name__ == '__main__':
logging.debug("Primer forward {} = {}".format(barcode, forward))
logging.debug("Primer reverse {} = {}".format(barcode, reverse))
os.system("mkdir -p {}/frogs".format(outdir))
cmd="mkdir -p {}/frogs".format(outdir)
out=runcmd(cmd)
# Extract Forward and Reverse Reads according to Primers (using cutadapt)
extractReads(inR1, inR2, outdir, forward, reverse, mismatch, tmpdir, trimreads)
#create frogs archive
cmd="cd {}/frogs; tar cvf samples.tar *_{{R1,R2}}.fastq.gz".format(outdir)
out=runcmd(cmd)
cmd="rm {}/frogs/*_{{R1,R2}}.fastq.gz".format(outdir)
out=runcmd(cmd)
logging.debug("End of processing")
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