def GC_Cleft(): liStrains = ['55-86_1','62-1041','CBS3082a','CBS3082b','77-1003','NCYC543','62-196','CBS6545','CBS6546','CBS6547','CBS6626','NRBC1892','CBS10367','CBS10368','CBS4104','68917-2','DBVPG4002','67-588','NRBC1811','NRBC10572','NRBC10955','NRBC101999','CBS10369','CBS5828','dd281a','CBS2861','CBS4568','DBVPG3452','DBVPG3108'] rep = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Nuclear/CleanPE" for strain in liStrains: repStrain = "%s/%s" % (rep,strain) seqStrain = "%s/cons%s.fasta" % (repStrain,strain) seqC = fasta.multiSeqEnVar(seqStrain,"Sakl0C") header = "cleft_%s" % strain fout = "%s/%s.fasta" % (repStrain,header) fasta.fromSeqToFasta(seqC[:989693],header,fout) print strain GC.txGC(seqC[:989693])
def decomposeChromos(): liStrains = ['55-86_1','62-1041','CBS3082a','CBS3082b','77-1003','NCYC543','62-196','CBS6545','CBS6546','CBS6547','CBS6626','NRBC1892','CBS10367','CBS10368','CBS4104','68917-2','DBVPG4002','67-588','NRBC1811','NRBC10572','NRBC10955','NRBC101999','CBS10369','CBS5828','dd281a','CBS2861','CBS4568','DBVPG3452','DBVPG3108'] rep = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Nuclear/CleanPE" for strain in liStrains: repStrain = "%s/%s" % (rep,strain) seqStrain = "%s/cons%s.fasta" % (repStrain,strain) seqA = fasta.multiSeqEnVar(seqStrain,"Sakl0A") seqB = fasta.multiSeqEnVar(seqStrain,"Sakl0B") seqC = fasta.multiSeqEnVar(seqStrain,"Sakl0C") seqD = fasta.multiSeqEnVar(seqStrain,"Sakl0D") seqE = fasta.multiSeqEnVar(seqStrain,"Sakl0E") seqF = fasta.multiSeqEnVar(seqStrain,"Sakl0F") seqG = fasta.multiSeqEnVar(seqStrain,"Sakl0G") seqH = fasta.multiSeqEnVar(seqStrain,"Sakl0H") headerA = "Sakl0A_%s" % strain headerB = "Sakl0B_%s" % strain headerC = "Sakl0C_%s" % strain headerD = "Sakl0D_%s" % strain headerE = "Sakl0E_%s" % strain headerF = "Sakl0F_%s" % strain headerG = "Sakl0G_%s" % strain headerH = "Sakl0H_%s" % strain foutA = "%s/%s.fasta" % (repStrain,headerA) foutB = "%s/%s.fasta" % (repStrain,headerB) foutC = "%s/%s.fasta" % (repStrain,headerC) foutD = "%s/%s.fasta" % (repStrain,headerD) foutE = "%s/%s.fasta" % (repStrain,headerE) foutF = "%s/%s.fasta" % (repStrain,headerF) foutG = "%s/%s.fasta" % (repStrain,headerG) foutH = "%s/%s.fasta" % (repStrain,headerH) fasta.fromSeqToFasta(seqA,headerA,foutA) fasta.fromSeqToFasta(seqB,headerB,foutB) fasta.fromSeqToFasta(seqC,headerC,foutC) fasta.fromSeqToFasta(seqD,headerD,foutD) fasta.fromSeqToFasta(seqE,headerE,foutE) fasta.fromSeqToFasta(seqF,headerF,foutF) fasta.fromSeqToFasta(seqG,headerG,foutG) fasta.fromSeqToFasta(seqH,headerH,foutH)