def defSimilarite(fic):
"""
"""
lines = open(fic,"r").read().split("\n")
for line in lines:
if line != "":
nsimg = "-"
nsimp = "-"
simg = "-"
simp = "-"
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
simg = string.atof(alignement.extrait_sim_needle("FastaGene/%s" % outf))
nsimg = alignement.extrait_nbsim_needle("FastaGene/%s" % outf)
nsimg = string.atof(nsimg)/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
simp = string.atof(alignement.extrait_sim_needle("FastaProt/%s" % outf))
nsimp = alignement.extrait_nbsim_needle("FastaProt/%s" % outf)
nsimp = string.atof(nsimp)/sizep*100
if simp != "-" and simg != "-":
print "%.1f\t%.1f\t%s\t%s\t%.1f\t%.1f\t" % (simg,simp,loc1,loc2,nsimg,nsimp)
else:
print "%s\t%s\t%s\t%s\t%s\t%s" % (simg,simp,loc1,loc2,nsimg,nsimp)
else:
print "\t\t%s\t%s" % (loc1,loc2)
def defSimilaritePseudo(fic):
"""
"""
lines = open(fic,"r").read().split("\n")
for line in lines:
if line != "":
nsimg = "-"
simg = "-"
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
simg = string.atof(alignement.extrait_sim_needle("Genes+Pseudos/%s" % outf))
nsimg = alignement.extrait_nbsim_needle("Genes+Pseudos/%s" % outf)
nsimg = string.atof(nsimg)/sizeg*100
if simg != "-":
print "%.1f\t%s\t%s\t%.1f\t" % (simg,loc1,loc2,nsimg)
else:
print "%s\t%s\t%s\t%s" % (simg,loc1,loc2,nsimg)
else:
print "\t\t%s\t%s" % (loc1,loc2)