def creeSequenceDeGene(scaff,deb,fin):
header = "%s %s %s" % (scaff,deb,fin)
filename = "%s-%s-%s.tfa" % (scaff,deb,fin)
ficScaff = "ScaffTfa/%s.tfa" % scaff
seq = fasta.seqEnVar(ficScaff)
seqGen = extraitSeqGene(seq,string.atoi(deb),string.atoi(fin))
if os.path.isfile(filename):
filename = "%s-2" % filename
fasta.fromSeqToFasta(seqGen,header,filename)
def creeSequenceDeGene(scaff,deb,fin,geneN,repGene,repSeq):
header = "%s-%s-%s" % (scaff,deb,fin)
filename = "%s/%s_%s-%s-%s.tfa" % (repGene,geneN,scaff,deb,fin)
ficScaff = "%s/%s.tfa" % (repSeq,scaff)
seq = fasta.seqEnVar(ficScaff)
seqGen = extraitSeqGene(seq,string.atoi(deb),string.atoi(fin))
if os.path.isfile(filename):
print "il existe deja"
if not os.path.isfile(filename):
fasta.fromSeqToFasta(seqGen,header,filename)
def GC_Cleft():
liStrains = ['55-86_1','62-1041','CBS3082a','CBS3082b','77-1003','NCYC543','62-196','CBS6545','CBS6546','CBS6547','CBS6626','NRBC1892','CBS10367','CBS10368','CBS4104','68917-2','DBVPG4002','67-588','NRBC1811','NRBC10572','NRBC10955','NRBC101999','CBS10369','CBS5828','dd281a','CBS2861','CBS4568','DBVPG3452','DBVPG3108']
rep = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Nuclear/CleanPE"
for strain in liStrains:
repStrain = "%s/%s" % (rep,strain)
seqStrain = "%s/cons%s.fasta" % (repStrain,strain)
seqC = fasta.multiSeqEnVar(seqStrain,"Sakl0C")
header = "cleft_%s" % strain
fout = "%s/%s.fasta" % (repStrain,header)
fasta.fromSeqToFasta(seqC[:989693],header,fout)
print strain
GC.txGC(seqC[:989693])
def creeSequenceDeGene(scaff, deb, fin, geneN, repGene, repSeq, long):
header = "%s" % (scaff)
filename = "%s/%s_%s-%s-%s.tfa" % (repGene, geneN, scaff, deb, fin)
ficScaff = "%s/%s.tfa" % (repSeq, scaff)
seq = fasta.seqEnVar(ficScaff)
seqGen = extraitSeqGene(seq, string.atoi(deb), string.atoi(fin)).upper()
# creation de la sequence uniquement si taille > a 98% de la sequence reference et si la taille est un multiple de 3
#if (len(seqGen) > long * 0.85 or len(seqGen) > 500) and len(seqGen) % 3 == 0:
if 1 == 1:
if os.path.isfile(filename):
print "il existe deja"
else:
seqGen = seqGen.replace("X", "N")
seqGen = seqGen.replace("S", "N")
seqGen = seqGen.replace("W", "N")
seqGen = seqGen.replace("R", "N")
seqGen = seqGen.replace("Y", "N")
seqGen = seqGen.replace("K", "N")
seqGen = seqGen.replace("M", "N")
fasta.fromSeqToFasta(seqGen, header, filename)
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 decomposeChromos():
liStrains = ['55-86_1','62-1041','CBS3082a','CBS3082b','77-1003','NCYC543','62-196','CBS6545','CBS6546','CBS6547','CBS6626','NRBC1892','CBS10367','CBS10368','CBS4104','68917-2','DBVPG4002','67-588','NRBC1811','NRBC10572','NRBC10955','NRBC101999','CBS10369','CBS5828','dd281a','CBS2861','CBS4568','DBVPG3452','DBVPG3108']
rep = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Nuclear/CleanPE"
for strain in liStrains:
repStrain = "%s/%s" % (rep,strain)
seqStrain = "%s/cons%s.fasta" % (repStrain,strain)
seqA = fasta.multiSeqEnVar(seqStrain,"Sakl0A")
seqB = fasta.multiSeqEnVar(seqStrain,"Sakl0B")
seqC = fasta.multiSeqEnVar(seqStrain,"Sakl0C")
seqD = fasta.multiSeqEnVar(seqStrain,"Sakl0D")
seqE = fasta.multiSeqEnVar(seqStrain,"Sakl0E")
seqF = fasta.multiSeqEnVar(seqStrain,"Sakl0F")
seqG = fasta.multiSeqEnVar(seqStrain,"Sakl0G")
seqH = fasta.multiSeqEnVar(seqStrain,"Sakl0H")
headerA = "Sakl0A_%s" % strain
headerB = "Sakl0B_%s" % strain
headerC = "Sakl0C_%s" % strain
headerD = "Sakl0D_%s" % strain
headerE = "Sakl0E_%s" % strain
headerF = "Sakl0F_%s" % strain
headerG = "Sakl0G_%s" % strain
headerH = "Sakl0H_%s" % strain
foutA = "%s/%s.fasta" % (repStrain,headerA)
foutB = "%s/%s.fasta" % (repStrain,headerB)
foutC = "%s/%s.fasta" % (repStrain,headerC)
foutD = "%s/%s.fasta" % (repStrain,headerD)
foutE = "%s/%s.fasta" % (repStrain,headerE)
foutF = "%s/%s.fasta" % (repStrain,headerF)
foutG = "%s/%s.fasta" % (repStrain,headerG)
foutH = "%s/%s.fasta" % (repStrain,headerH)
fasta.fromSeqToFasta(seqA,headerA,foutA)
fasta.fromSeqToFasta(seqB,headerB,foutB)
fasta.fromSeqToFasta(seqC,headerC,foutC)
fasta.fromSeqToFasta(seqD,headerD,foutD)
fasta.fromSeqToFasta(seqE,headerE,foutE)
fasta.fromSeqToFasta(seqF,headerF,foutF)
fasta.fromSeqToFasta(seqG,headerG,foutG)
fasta.fromSeqToFasta(seqH,headerH,foutH)
