def pipeIncompForAssembly(strain,out):
reads = "/Volumes/BioSan/Users/friedrich/Incompatibilite/Reads/%s/NG-5435_%s_sequence.fastq" % (strain,strain[:-2])
repOut = "/Volumes/BioSan/Users/friedrich/Incompatibilite/BWA/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/Incompatibilite/ReferenceSequence/FY/Index/BWA/FYref.tfa"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
opt = "-n 0 -o 0"
ficSam = traitementBWA.lanceBWAsamse(strain,out,reads,repOut,ref,opt)
ficSamX = traitementSamtools.convertFlag(ficSam)
lUnmappedReads = traitementBWA.extraitUnmappedReads(ficSam,reads)
def mappingSaklCleanSEOld(strain):
reads = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanSE30strains/s_%s-trim.fq" % (strain)
if not os.path.isfile(reads):
reads = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanSE30strains/Run3/s_%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 reads:
opt += "-I "
print reads
ficSam = traitementBWA.lanceBWAsamse(outBWA, reads, repOut, ref, opt)
# ficSam = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/NuclearMito/55-86_1/aln_55-86_1SE.sam"
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
ficSamX = traitementSamtools.convertFlag(ficSamInRef)
unmappedReads = traitementBWA.extraitUnmappedReads(ficSamX, reads)
