def defNouvelIdent(fic): """ """ lines = open(fic,"r").read().split("\n") for line in lines: if line != "": nidg = "-" nidp = "-" idg = "-" idp = "-" lis = line.split("\t") loc1 = lis[0] loc2 = lis[2] if loc1 != "" and loc2 != "": ficg1 = "FastaGene/%s.tfa" % loc1 ficg2 = "FastaGene/%s.tfa" % loc2 ficp1 = "FastaProt/%s.tfa" % loc1 ficp2 = "FastaProt/%s.tfa" % loc2 outf = "%s-%s.needle" % (files.get_name(ficg1).lower(),files.get_name(ficg2).lower()) if os.path.isfile("FastaGene/%s" % outf): sizeg1 = len(fasta.seqEnVar(ficg1)) sizeg2 = len(fasta.seqEnVar(ficg2)) if sizeg1 > sizeg2: sizeg = sizeg2 else: sizeg = sizeg1 idg = string.atof(alignement.extrait_id_needle("FastaGene/%s" % outf)) nidg = alignement.extrait_nbid_needle("FastaGene/%s" % outf) nidg = string.atof(nidg)/sizeg*100 if os.path.isfile("FastaProt/%s" % outf): sizep1 = len(fasta.seqEnVar(ficp1)) sizep2 = len(fasta.seqEnVar(ficp2)) if sizep1 > sizep2: sizep = sizep2 else: sizep = sizep1 idp = string.atof(alignement.extrait_id_needle("FastaProt/%s" % outf)) nidp = alignement.extrait_nbid_needle("FastaProt/%s" % outf) nidp = string.atof(nidp)/sizep*100 if idp != "-" and idg != "-": print "%.1f\t%.1f\t%s\t%s\t%.1f\t%.1f\t" % (idg,idp,loc1,loc2,nidg,nidp) else: print "%s\t%s\t%s\t%s\t%s\t%s" % (idg,idp,loc1,loc2,nidg,nidp) else: print "\t\t%s\t%s" % (loc1,loc2)
def defNouvelIdentncRNA(fic): """ """ lines = open(fic,"r").read().split("\n") for line in lines: if line != "": nidg = "-" idg = "-" lis = line.split("\t") loc1 = lis[0] loc2 = lis[2] if loc1 != "" and loc2 != "": ficg1 = "Genes+Pseudos/%s.tfa" % loc1 ficg2 = "Genes+Pseudos/%s.tfa" % loc2 outf = "%s-%s.needle" % (files.get_name(ficg1).lower(),files.get_name(ficg2).lower()) if not os.path.isfile("Genes+Pseudos/%s" % outf): alignement.ali_needle(ficg1,ficg2) sizeg1 = len(fasta.seqEnVar(ficg1)) sizeg2 = len(fasta.seqEnVar(ficg2)) if sizeg1 > sizeg2: sizeg = sizeg2 else: sizeg = sizeg1 idg = string.atof(alignement.extrait_id_needle("Genes+Pseudos/%s" % outf)) nidg = alignement.extrait_nbid_needle("Genes+Pseudos/%s" % outf) nidg = string.atof(nidg)/sizeg*100 if idg != "-": print "%.1f\t%s\t%s\t%.1f\t" % (idg,loc1,loc2,nidg) else: print "%s\t%s\t%s\t%s" % (idg,loc1,loc2,nidg) else: print "\t\t%s\t%s" % (loc1,loc2)