def identifyScaffChimereBU(species,infile,rep = "."):
# tentative d amelioration de la routine de mise en evidence des scaff chimeres
# resultats non probants!!
# qd matche d une meme position sur un scaffold, voulais garder celui qui a le meilleur score uniquement, mais on observe souvent
# soit des scores identiques soit des scores + grands pour les genes issus des chromo differents
# du coup, les resultats sont limites pires!!
# peut etre vaut il mieux post-traiter les resultats issus de la 1ere routine
os.chdir(rep)
allScaff = fasta.fromFastaToDico(infile)
outfile = infile.replace(".fasta","_chimere.log")
of = open(outfile,"w")
print species
if species.lower() == "sace":
db = "/Volumes/BioSan/Users/friedrich/BlastDB/Peptidic/Sace/s288c.pep"
elif species.lower() == "lakl" or species.lower() == "sakl":
db = "/Volumes/BioSan/Users/friedrich/BlastDB/Peptidic/Sakl/saklRef.pep"
else:
print "Species name not understood. Should be Sace, Sakl or Lakl"
sys.exit()
for scaff in allScaff.keys():
if len(allScaff[scaff]) > 1000:
fileN = "%s.fasta" % scaff
fasta.fromSeqToFasta(allScaff[scaff],scaff,fileN)
fileO = fileN.replace("fasta","blastx")
alignement.run_blastxFmt(fileN,fileO,db,1000)
if os.path.isfile(fileO):
lines = open(fileO,"r").read().split("\n")
chimere = 0
dicProt = {}
dicProtScore = {}
for line in lines:
if line != "":
el = line.split("\t")
if string.atof(el[2]) > 95 and string.atof(el[3]) > 70:
if string.atoi(el[6]) in dicProt:
prot = dicProt[string.atoi(el[6])]
score = dicProtScore[prot]
if score < string.atof(el[11]):
del dicProt[string.atoi(el[6])]
dicProt[string.atoi(el[6])] = el[1]
dicProtScore[el[1]] = string.atof(el[11])
else:
dicProt[string.atoi(el[6])] = el[1]
dicProtScore[el[1]] = string.atof(el[11])
lChr = []
for key in dicProt.keys():
if species.lower() == "sace":
if dicProt[key][0:2] not in lChr:
lChr.append(dicProt[key][0:2])
else:
if dicProt[key][0:6] not in lChr:
lChr.append(dicProt[key][0:6])
# si on a plus de 1 chromo dans la liste, on a a faire a un scaff chimere
if len(lChr) > 1:
lProt = dicProt.items()
lProt.sort()
print "%s - %s bp" % (scaff,len(allScaff[scaff]))
of.write("%s - %s bp\n" % (scaff,len(allScaff[scaff])))
print lProt
of.write("%s\n" % lProt)
fileO2 = fileO.replace("blastx","blastx-std")
alignement.run_blastx(fileN,fileO2,db,1000)
else:
os.remove(fileO)
os.remove(fileN)
of.close()
def identifyScaffChimere(species,infile,rep = "."):
os.chdir(rep)
allScaff = fasta.fromFastaToDico(infile)
#outfile = infile.replace(".fasta","_chimere.log")
## RUN 25 Strains ##
outfile = infile.replace(".scafSeq","_chimere.log")
##
of = open(outfile,"w")
print species
if species.lower() == "sace":
db = "/Volumes/BioSan/Users/friedrich/BlastDB/Peptidic/Sace/s288c.pep"
elif species.lower() == "lakl" or species.lower() == "sakl":
db = "/Volumes/BioSan/Users/friedrich/BlastDB/Peptidic/Sakl/saklRef.pep"
else:
print "Species name not understood. Should be Sace, Sakl or Lakl"
sys.exit()
for scaff in allScaff.keys():
if len(allScaff[scaff]) > 1000:
fileN = "%s.fasta" % scaff
fasta.fromSeqToFasta(allScaff[scaff],scaff,fileN)
fileO = fileN.replace("fasta","blastx")
alignement.run_blastxFmt(fileN,fileO,db,1000)
if os.path.isfile(fileO):
lines = open(fileO,"r").read().split("\n")
chr = ""
chimere = 0
dicProt = {}
lP1 = []
lP2 = []
for line in lines:
if line != "":
el = line.split("\t")
#if string.atof(el[2]) > 90 and string.atof(el[3]) > 50:
if string.atof(el[2]) > 95 and string.atof(el[3]) > 70:
dicProt[el[1]] = string.atoi(el[6])
if chr == "":
if species.lower() == "sace":
chr = el[1][0:2]
else:
chr = el[1][0:6]
if string.atoi(el[6]) not in lP1:
lP1.append(string.atoi(el[6]))
elif el[1][0:2] != chr and el[1][0:6] != chr:
chimere = 1
if string.atoi(el[6]) not in lP2:
lP2.append(string.atoi(el[6]))
else:
if string.atoi(el[6]) not in lP1:
lP1.append(string.atoi(el[6]))
if chimere == 1:
# ne tient pas compte des scaffs pour lesquels chimerisation due a la presence d un paralogue
chimere = 0
if len(lP1) < len(lP2):
for p1 in lP1:
if p1 not in lP2:
chimere = 1
else:
for p2 in lP2:
if p2 not in lP1:
chimere = 1
if chimere == 1:
lProt = dicProt.items()
lProt.sort(cmpval)
pos = 0
lchrom = []
# variable toR indique s il est possible de retirer la derniere valeur de la liste ou non
#print "%s - %s bp" % (scaff,len(allScaff[scaff]))
#print lProt
toR = 0
for prot in lProt:
#print prot
if prot[1] > pos:
if species.lower() == "sace":
if prot[0][0:2] not in lchrom:
lchrom.append(prot[0][0:2])
toR = 1
else:
if prot[0][0:6] not in lchrom:
lchrom.append(prot[0][0:6])
toR = 1
pos = prot[1]
#print lchrom
# les donnees etant triees
# si la valeur n est pas superieure, c est qu elle est egale
else:
if toR == 1:
# je retire le dernier chromo mis dans la liste
# ma liste ne contient aucune info par rapport au paralogue qui sont situees a la meme position
lchrom.pop()
# il faut que j ote la possibilite de remover pour le prochain tour, au cas ou on a + de 2 paralogues identifies a la meme position
toR = 0
list(set(lchrom))
if species.lower() == "sace":
firstChrom = lProt[0][0][0:2]
lastChrom = lProt[-1][0][0:2]
else:
firstChrom = lProt[0][0][0:6]
lastChrom = lProt[-1][0][0:6]
#if len(lchrom) > 1 and firstChrom != lastChrom:
if len(lchrom) > 1:
print "%s - %s bp" % (scaff,len(allScaff[scaff]))
of.write("%s - %s bp\n" % (scaff,len(allScaff[scaff])))
print lProt
of.write("%s\n" % lProt)
fileO2 = fileO.replace("blastx","blastx-std")
alignement.run_blastx(fileN,fileO2,db,1000)
else:
os.remove(fileO)
os.remove(fileN)
else:
os.remove(fileO)
os.remove(fileN)
of.close()
def stats4StrainsALarrache(suff,outfile = ""):
if outfile != "":
of = open(outfile, 'a')
fileP = "AliProt/%s-4strains.fasta" % suff
aliP = fasta.fromFastaToDico(fileP)
lSeqILP = list()
for seqNP in aliP.keys():
if "IL01" in seqNP:
lSeqILP.append(seqNP)
seqRefP = aliP[suff]
nbDiffP = 0
lgILP = 0
for seqILnP in lSeqILP:
print "%s\t%s" % (suff,seqILnP)
seqILP = aliP[seqILnP]
lgILP += len(string.replace(seqILP,"-",""))
for i in range(0, len(seqILP)):
if seqILP[i] != seqRefP[i] and seqILP[i] != "-":
aVerif = 0
resWE = ""
resNC = ""
resYJM = ""
# opt1 symbolise le fait que IL = WE ou IL = NC
opt1 = 0
# opt2 symbolise la fait que YJM = FY
opt2 = 0
# opt3 symbolise notre profile recherche, IL = YJM et diff des 3 autres
opt3 = 0
for (seqNP,sequenceP) in aliP.items():
if "IL01" in seqNP:
if sequenceP[i] == seqRefP[i]:
aVerif = 1
else:
#aVerif = 0
if "YJM981" in seqNP:
if sequenceP[i] != "-":
if resYJM == "":
resYJM = sequenceP[i]
elif resYJM != sequenceP[i]:
resYJM = "ambigue"
if "WE372" in seqNP:
if sequenceP[i] != "-":
if resWE == "":
resWE = sequenceP[i]
elif resWE != sequenceP[i]:
resWE = "ambigue"
if "NC02" in seqNP:
if sequenceP[i] != "-":
if resNC == "":
resNC = sequenceP[i]
elif resNC != sequenceP[i]:
resNC = "ambigue"
#print "%s, %s, %s, %s, %s" % (seqILP[i],resWE,resNC,resYJM,seqRefP[i])
if aVerif == 1:
if outfile == "":
print "%s\t%s\tposition a verifier pour chevauchement IL01" % (suff,i+1)
else:
of.write("%s\t%s\tposition a verifier pour chevauchement IL01\n" % (suff,i+1))
else:
if resWE != "-":
if seqILP[i] == resWE:
opt1 = 1
if resNC != "-":
if seqILP[i] == resNC:
opt1 = 1
if resYJM != "-":
if seqRefP[i] == resYJM:
opt2 = 1
elif seqILP[i] == resYJM:
if opt1 == 0:
opt3 = 1
nbDiffP += 1
if outfile == "":
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (suff,i+1,seqILP[i],seqRefP[i],resWE,resNC,resYJM,opt1,opt2,opt3)
else:
of.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (suff,i+1,seqILP[i],seqRefP[i],resWE,resNC,resYJM,opt1,opt2,opt3))
if outfile != "":
of.close()
def statsALarrache(suff,outfile = ""):
if outfile != "":
of = open(outfile, 'a')
fileP = "AliProt/%s-11strains.fasta" % suff
fileG = "AliGene/%s-G-11strains.fasta" % suff
#fileP = "AliProt/%s-4strains.fasta" % suff
#fileG = "AliGene/%s-G-4strains.fasta" % suff
aliP = fasta.fromFastaToDico(fileP)
lSeqILP = list()
for seqNP in aliP.keys():
if "IL01" in seqNP:
lSeqILP.append(seqNP)
if outfile == "":
print "\nTraite %s:\n----Alignement des proteines----\non a %s sequence de IL01" % (suff,len(lSeqILP))
else:
of.write("\nTraite %s:\n----Alignement des proteines----\non a %s sequence de IL01\n" % (suff,len(lSeqILP)))
# recuperation de l alignement de la reference
seqRefP = aliP[suff]
nbDiffP = 0
nbDiffPIsolee = 0
lgILP = 0
for seqILnP in lSeqILP:
if outfile == "":
print "+++traite %s+++" % seqILnP
else:
of.write("+++traite %s+++\n" % seqILnP)
seqILP = aliP[seqILnP]
lgILP += len(string.replace(seqILP,"-",""))
for i in range(0, len(seqILP)):
if seqILP[i] != seqRefP[i] and seqILP[i] != "-":
# je peux recuperer le nombre de positions differentes, leur localisation
# le nombre de position isolee
lSeqIdP = list()
for (seqNP,sequenceP) in aliP.items():
if "IL01" in seqNP:
if sequenceP[i] == seqRefP[i]:
aVerif = 1
break
else:
aVerif = 0
if sequenceP[i] == seqILP[i]:
lSeqIdP.append(seqNP)
if aVerif == 1:
if outfile == "":
print "%s : position a verifier pour chevauchement IL01" % (i+1)
else:
of.write("%s : position a verifier pour chevauchement IL01\n" % (i+1))
else:
nbDiffP += 1
if len(lSeqIdP) == 0:
nbDiffPIsolee += 1
if outfile == "":
print "%s\t%s\t%s\n" % (i+1,len(lSeqIdP),lSeqIdP)
else:
of.write("%s\t%s\t%s\n" % (i+1,len(lSeqIdP),lSeqIdP))
#print "%s\t%s\t%s\t%s\t%s" % (suff,len(string.replace(seqRefP,"-","")),lgILP,nbDiffP,nbDiffPIsolee)
aliG = fasta.fromFastaToDico(fileG)
lSeqILG = list()
for seqNG in aliG.keys():
if "IL01" in seqNG:
lSeqILG.append(seqNG)
if outfile == "":
print "----Alignement des genes----\non a ",len(lSeqILG)," sequence de IL01"
else:
of.write("----Alignement des genes----\non a %s sequence de IL01\n" % len(lSeqILG))
# recuperation de l alignement de la reference
seqRefG = aliG[suff]
nbDiffG = 0
nbDiffGIsolee = 0
lgILG = 0
for seqILnG in lSeqILG:
if outfile == "":
print "+++traite %s+++" % seqILnG
else:
of.write("+++traite %s+++\n" % seqILnG)
seqILG = aliG[seqILnG]
lgILG += len(string.replace(seqILG,"-",""))
for i in range(0, len(seqILG)):
if seqILG[i].upper() != seqRefG[i].upper() and seqILG[i] != "-":
lSeqIdG = list()
for (seqNG,sequenceG) in aliG.items():
if "IL01" in seqNG:
if sequenceG[i].upper() == seqRefG[i].upper():
aVerif = 1
break
else:
aVerif = 0
if sequenceG[i].upper() == seqILG[i].upper():
lSeqIdG.append(seqNG)
if aVerif == 1:
if outfile == "":
print "%s : position a verifier pour chevauchement IL01" % (i+1)
else:
of.write("%s : position a verifier pour chevauchement IL01\n" % (i+1))
else:
nbDiffG += 1
if len(lSeqIdG) == 0:
nbDiffGIsolee += 1
if outfile == "":
print "%s\t%s\t%s" % (i+1,len(lSeqIdG),lSeqIdG)
else:
of.write("%s\t%s\t%s\n" % (i+1,len(lSeqIdG),lSeqIdG))
if outfile != "":
of.close()
#print "%s\t%s\t%s\t%s\t%s" % (suff,len(string.replace(seqRefG,"-","")),lgILG,nbDiffG,nbDiffGIsolee)
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (suff,len(string.replace(seqRefP,"-","")),len(lSeqILP),lgILP,nbDiffP,nbDiffPIsolee,len(string.replace(seqRefG,"-","")),len(lSeqILG),lgILG,nbDiffG,nbDiffGIsolee)
def longScaff(infile):
allSeq = fasta.fromFastaToDico(infile)
for scaff in allSeq.keys():
print "%s\t%s" % (scaff,len(allSeq[scaff]))
