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)
