Commit 9c75308c authored by Laure QUINTRIC's avatar Laure QUINTRIC

format data for frogs

parent b050b138
......@@ -136,9 +136,9 @@ def extractReads(inR1, inR2, outdir, forward, reverse, mismatch, tmpdir, trimrea
R2repairedF= R2cutadaptoutnameF.replace("-cutadapt", "")
rePairReads(outdir, R1repairedR, R2repairedF , singletons, R1cutadaptoutnameR, R2cutadaptoutnameF)
cmd = "zcat {} {} > {}/frogs/{} ; gzip {}/frogs/{}".format(R1repairedF, R2repairedF, outdir, R1repairedF.replace("_R1F", "_R1"), outdir, R1repairedF.replace("_R1F", "_R1"))
cmd = "zcat {} {} > {}/frogs/{} ; gzip {}/frogs/{}".format(R1repairedF, R2repairedF, outdir, os.path.basename(R1repairedF.replace("_R1F", "_R1")), outdir, os.path.basename(R1repairedF.replace("_R1F", "_R1")))
out = runcmd(cmd)
cmd = "zcat {} {} > {}/frogs/{} ; gzip {}/frogs/{}".format(R1repairedR, R2repairedR, outdir, R1repairedR.replace("_R1R", "_R2"), outdir, R1repairedR.replace("_R1R", "_R2"))
cmd = "zcat {} {} > {}/frogs/{} ; gzip {}/frogs/{}".format(R1repairedR, R2repairedR, outdir, os.path.basename(R1repairedR.replace("_R1R", "_R2")), outdir, os.path.basename(R1repairedR.replace("_R1R", "_R2")))
out = runcmd(cmd)
def runCutadapt(primerseq, mismatch, outfile, samplename, infile, tmpdir, trimreads) :
......
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