def mappingSaklCleanSE(strain):
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanPE/s_1_%s-trim.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanPE/s_2_%s-trim.fq" % (strain)
if not os.path.isfile(reads1):
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run3/CleanPE/s_1_%s-trim.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run3/CleanPE/s_2_%s-trim.fq" % (strain)
repOut = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/NuclearMito/%s" % (strain)
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Index/BWA/saklRefNuclMito.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
outBWA = "aln_%s" % strain
opt = "-n 8 -o 2 "
if not "Run3" in reads1:
opt += "-I "
# print reads
ficSam = traitementBWA.lanceBWA(outBWA, reads1, reads2, repOut, ref, opt)
# conversion du ficSam traditionnel en ficSam avec Flags textuels
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
ficSamNotInRef = ficSamInRef.replace("inRef", "notInRef")
ficSamX = traitementSamtools.convertFlag(ficSamNotInRef)
traitementBWA.extraitPEUnmappedReads(ficSamX, reads1, reads2)
def extraitUnmappedCleanSE(strain):
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanPE/s_1_%s-trim.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanPE/s_2_%s-trim.fq" % (strain)
if not os.path.isfile(reads1):
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run3/CleanPE/s_1_%s-trim.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run3/CleanPE/s_2_%s-trim.fq" % (strain)
repOut = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/NuclearMito/%s" % (strain)
ficSamInRef = "%s/aln_%sPE.sam.inRef" % (repOut, strain)
ficSamNotInRef = ficSamInRef.replace("inRef", "notInRef")
ficSamX = traitementSamtools.convertFlag(ficSamNotInRef)
traitementBWA.extraitPEUnmappedReads(ficSamX, reads1, reads2)