def pipeSaklSE(strain, p1, p2): reads = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run5/s_%s_all-trim.fq" % (strain) repOut = "/Volumes/BioSan/Users/pjung/Documents/GB-3G/BWA/Nuclear/Recombinaison/%s" % strain ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Index/BWA/saklRef.fasta" if not os.path.isdir(repOut): os.mkdir(repOut) cmdA = "chmod 777 %s" % repOut os.system(cmdA) outBWA = "aln_%s" % strain opt = "" if not "Run3" in reads and not "Run4" in reads and not "Run5" in reads: opt += "-I" opt += " -n 5 -o 1" ficSam = traitementBWA.lanceBWAsamse(outBWA, reads, repOut, ref, opt) ficVarFilter = traitementSamtools.lancePipeSamtoolsRecomb(ficSam, ref) ficOri = definiProvenanceSeg(strain, p1, p2) #ficOri = "ori81b.tab" ficOriNew = postTraiteProvenanceSeg(ficOri, strain)
def pipeSaklPE(strain, p1, p2): reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run6/CleanPE/s_1_%s-trim.fq" % (strain) reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run6/CleanPE/s_2_%s-trim.fq" % (strain) repOut = "/Volumes/BioSan/Users/pjung/Documents/GB-3G/BWA/Nuclear/Recombinaison/%s" % strain ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Index/BWA/saklRef.fasta" if not os.path.isdir(repOut): os.mkdir(repOut) cmdA = "chmod 777 %s" % repOut os.system(cmdA) outBWA = "aln_%s_1" % strain opt = "" if not "Run3" in reads1 and not "Run4" in reads1: opt += "-I" opt += " -n 8 -o 2" ficSam = traitementBWA.lanceBWA(outBWA, reads1, reads2, repOut, ref, opt) ficVarFilter = traitementSamtools.lancePipeSamtoolsRecomb(ficSam, ref) ficOri = definiProvenanceSeg(strain, p1, p2) ficOriNew = postTraiteProvenanceSeg(ficOri, strain)