Commit 8ce55c12 authored by Laure QUINTRIC's avatar Laure QUINTRIC

format data for frogs

parent 95ea5e09
......@@ -134,11 +134,11 @@ def extractReads(inR1, inR2, outdir, forward, reverse, mismatch, tmpdir, trimrea
singletons="{}/{}_R1R-R2Fsingletons.fastq.gz".format(outdir, couplename)
R1repairedR= R1cutadaptoutnameR.replace("-cutadapt", "")
R2repairedF= R2cutadaptoutnameF.replace("-cutadapt", "")
rePairReads(outdir, R1repaired, R2repaired , singletons, R1cutadaptoutnameR, R2cutadaptoutnameF)
rePairReads(outdir, R1repairedR, R2repairedF , singletons, R1cutadaptoutnameR, R2cutadaptoutnameF)
cmd = "zcat {} {} > {} ; gzip {}".format(R1repairedF, R2repairedF, R1repairedF.replace("_R1F", "R1"), R1repairedF.replace("_R1F", "R1"))
out = runcmd(cmd)
cmd = "zcat {} {} > {} ; gzip {}".format(R1repairedF, R2repairedF, R1repairedF.replace("_R1F", "R1"), R1repairedF.replace("_R1F", "R1"))
cmd = "zcat {} {} > {} ; gzip {}".format(R1repairedR, R2repairedR, R1repairedR.replace("_R1R", "R2"), R1repairedR.replace("_R1R", "R2"))
out = runcmd(cmd)
def runCutadapt(primerseq, mismatch, outfile, samplename, infile, tmpdir, trimreads) :
......
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