def verifIdent(fic):
"""
"""
ficOut = "outest.txt"
f = open(ficOut,"w")
lines = open(fic,"r").read().split("\n")
for line in lines:
if line != "":
idg = "-"
idp = "-"
lis = line.split("\t")
loc1 = lis[0]
loc2 = lis[1]
if loc1 != "" and loc2 != "":
ficg1 = "FastaGene/%s.tfa" % loc1
ficg2 = "FastaGene/%s.tfa" % loc2
ficp1 = "FastaProt/%s.tfa" % loc1
ficp2 = "FastaProt/%s.tfa" % loc2
if os.path.isfile(ficg1) and os.path.isfile(ficg2):
alignement.ali_needle(ficg1,ficg2)
idg = alignement.extrait_id_needle("FastaGene/%s-%s.needle" % (files.get_name(ficg1).lower(),files.get_name(ficg2).lower()))
if os.path.isfile(ficp1) and os.path.isfile(ficp2):
alignement.ali_needle(ficp1,ficp2)
idp = alignement.extrait_id_needle("FastaProt/%s-%s.needle" % (files.get_name(ficp1).lower(),files.get_name(ficp2).lower()))
f.write("%s\t%s\t%s\t%s\n" % (loc1,loc2,idg,idp))
f.close
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 calcIdent(fic):
"""
"""
if os.path.isdir(fic):
allfile = glob.glob("%s/*.tfa" % fic)
fout = "ficOut"
f = open(fout,"w")
f.write("el1\tel2\tid\tsim\n")
listFic = allfile
for file in allfile :
f1 = listFic[0]
listFic = listFic[1:]
for f2 in listFic:
#ficg1 = "FastaGene/%s.tfa" % loc1[0:-1]
#ficg2 = "FastaGene/%s.tfa" % loc2[0:-1]
#ficp1 = "FastaProt/%s.tfa" % loc1[0:-1]
#ficp2 = "FastaProt/%s.tfa" % loc2[0:-1]
name = "%s-%s.needle" % (files.get_name(f1).lower(),files.get_name(f2).lower())
outfile = "%s/%s" % (fic, name)
if not os.path.isfile(outfile):
alignement.ali_needle(f1,f2,outfile)
if os.path.isfile(outfile):
id = alignement.extrait_id_needle(outfile)
sim = alignement.extrait_sim_needle(outfile)
f.write("%s\t%s\t%s\t%s\n" % (files.get_name(f1),files.get_name(f2),id,sim))
f.close()
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)
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)