def definiAllele(fic,database):
"""
"""
totg = 0
g = 0
totp = 0
lines = open(fic,"r").read().split("\n")
for line in lines:
if line != "":
lis = line.split("\t")
def1 = lis[0]
loc1 = lis[1]
def2 = lis[2]
loc2 = lis[3]
if loc1 != "" and loc2 != "":
ficg1 = "FastaGene/%s.tfa" % loc1
ficg2 = "FastaGene/%s.tfa" % loc2
ficp1 = "FastaProt/%s.tfa" % loc1
ficp2 = "FastaProt/%s.tfa" % loc2
elif loc1 != "" and def1 == "noSim":
ficin = "FastaGene/%s.tfa" % loc1
ficout = "FastaGene/%s.blastn" % files.get_name(ficin).lower()
if not os.path.isfile(ficout):
alignement.run_blastn(ficin, ficout, database)
if os.path.isfile(ficout):
lis = open(ficout,"r").read().split("\n")
if len(lis) == 2:
inf1 = "noSim"
else:
det = lis[1].split("\t")
if string.atof(det[2]) > 70:
inf1 = "%s-%s" % (det[1].split("|")[-1],det[2])
else :
inf1 = "soSignSim"
print "%s\t%s" % (loc1,inf1)
continue
elif loc2 != "" and def2 == "noSim":
ficin = "FastaGene/%s.tfa" % loc2
ficout = "FastaGene/%s.blastn" % files.get_name(ficin).lower()
alignement.run_blastn(ficin, ficout, database)
if os.path.isfile(ficout):
lis = open(ficout,"r").read().split("\n")
if len(lis) == 2:
inf1 = "noSim"
else:
det = lis[1].split("\t")
if string.atof(det[2]) > 70:
inf1 = "%s-%s" % (det[1].split("|")[-1],det[2])
else :
inf1 = "soSignSim"
print "%s\t%s" % (loc2,inf1)
continue
elif loc1 != "":
ficg1 = "FastaGene/%s.tfa" % loc1
loc2 = def1.split("-")[0]
ficg2 = "FastaGene/%s.tfa" % loc2
ficp1 = "FastaProt/%s.tfa" % loc1
ficp2 = "FastaProt/%s.tfa" % loc2
elif loc2 != "":
ficg1 = "FastaGene/%s.tfa" % loc2
loc1 = def2.split("-")[0]
ficg2 = "FastaGene/%s.tfa" % loc1
ficp1 = "FastaProt/%s.tfa" % loc2
ficp2 = "FastaProt/%s.tfa" % loc1
outf = "%s-%s.needle" % (files.get_name(ficg1).lower(),files.get_name(ficg2).lower())
if not os.path.isfile("FastaGene/%s" % outf):
alignement.ali_needle(ficg1,ficg2)
if not os.path.isfile("FastaProt/%s" % outf):
alignement.ali_needle(ficp1,ficp2)
idg = alignement.extrait_id_needle("FastaGene/%s" % outf)
idp = alignement.extrait_id_needle("FastaProt/%s" % outf)
if idg == "100":
suf = 1
else:
if idg > 70:
suf = 2
totg = totg + string.atof(idg)
g = g + 1
totp = totp + string.atof(idp)
print "%s\t%s\t%s\t%s" % (loc1,loc2,idg,idp)
print "\nMoyenne des pourcentages d identite (sans tenir compte des 100%)"
print "au niveau des genes : %s" % (totg/g)
print "au niveau des proteines: %s" % (totp/g)
def compAnnot(fic,database):
"""
"""
totg = 0
g = 0
totp = 0
lines = open(fic,"r").read().split("\n")
for line in lines:
if line != "":
idg = "-"
idp = "-"
lis = line.split("\t")
type1 = lis[0]
type2 = lis[9]
annot1 = lis[1]
annot2 = lis[10]
loc1 = lis[2]
loc2 = lis[11]
orf1 = lis[3]
orf2 = lis[12]
deb1 = lis[4]
deb2 = lis[13]
fin1 = lis[5]
fin2 = lis[14]
long1 = lis[6]
long2 = lis[15]
sens1 = lis[7]
sens2 = lis[16]
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 not os.path.isfile("FastaGene/%s" % outf):
if os.path.isfile(ficg1) and os.path.isfile(ficg2):
alignement.ali_needle(ficg1,ficg2)
if not os.path.isfile("FastaProt/%s" % outf):
if os.path.isfile(ficp1) and os.path.isfile(ficp2):
alignement.ali_needle(ficp1,ficp2)
if os.path.isfile("FastaGene/%s" % outf):
idg = alignement.extrait_id_needle("FastaGene/%s" % outf)
if os.path.isfile("FastaProt/%s" % outf):
idp = alignement.extrait_id_needle("FastaProt/%s" % outf)
if idg == "100":
suf = 1
else:
suf = 2
if idg != "-":
totg = totg + string.atof(idg)
g = g + 1
totp = totp + string.atof(idp)
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t\t%s\t%s\t\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (type1,annot1,loc1,orf1,deb1,fin1,long1,sens1,idg,idp,type2,annot2,loc2,orf2,deb2,fin2,long2,sens2,suf)
continue
else:
suf = ""
idg = ""
idp = ""
inf1 = ""
inf2 = ""
# si n est pas un allele evident, je lance mon gene contre ma banque complete pour voir si y aurait pas une similarite significative
if loc1 != "":
ficin = "FastaGene/%s.tfa" % loc1
if os.path.isfile(ficin):
ficout = "FastaGene/%s.blastn" % files.get_name(ficin).lower()
alignement.run_blastn(ficin, ficout, database)
if os.path.isfile(ficout):
lis = open(ficout,"r").read().split("\n")
if len(lis) == 2:
inf1 = "noSim"
else:
det = lis[1].split("\t")
inf1 = "%s-%s" % (det[1].split("|")[-1],det[2])
if loc2 != "":
ficin = "FastaGene/%s.tfa" % loc2
if os.path.isfile(ficin):
ficout = "FastaGene/%s.blastn" % files.get_name(ficin).lower()
alignement.run_blastn(ficin, ficout, database)
if os.path.isfile(ficout):
lis = open(ficout,"r").read().split("\n")
if len(lis) == 2:
inf2 = "noSim"
else:
det = lis[1].split("\t")
inf2 = "%s-%s" % (det[1].split("|")[-1],det[2])
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t\t\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (type1,annot1,loc1,orf1,deb1,fin1,long1,sens1,inf1,inf2,type2,annot2,loc2,orf2,deb2,fin2,long2,sens2)
print "\nMoyenne des pourcentages d identite (sans tenir compte des 100%)"
print "au niveau des genes : %s" % (totg/g)
print "au niveau des proteines: %s" % (totp/g)
