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)