def fromVarfilter2tsvLikeCyrielle(ficVar):
print ficVar
ficSnp = traitementSamtools.decomposeVarfilter(ficVar)
ficTsv = "%s.tsv" % ficSnp
of = open(ficTsv, "w")
fM = open(ficSnp, "r")
line = fM.readline()
while line:
el = line.split("\t")
# ne tient pas compte des indels etc dans la ligne
#print "---%s---" % el
while string.find(el[8], "^") != -1:
el[8] = string.replace(el[8], el[8][string.find(el[8], "^"):string.find(el[8], "^") + 2], "")
while string.find(el[8], "+") != -1:
el[8] = string.replace(el[8], el[8][string.find(el[8], "+"):string.find(el[8], "+") + string.atoi(
el[8][string.find(el[8], "+") + 1]) + 2], "")
while string.find(el[8], "-") != -1:
el[8] = string.replace(el[8], el[8][string.find(el[8], "-"):string.find(el[8], "-") + string.atoi(
el[8][string.find(el[8], "-") + 1]) + 2], "")
nbA = el[8].count("A") + el[8].count("a")
nbG = el[8].count("G") + el[8].count("g")
nbC = el[8].count("C") + el[8].count("c")
nbT = el[8].count("T") + el[8].count("t")
cov = string.atof(el[7])
nbRef = el[8].count(".") + el[8].count(",")
if el[2] == "a" or el[2] == "A":
nbA = nbRef
elif el[2] == "g" or el[2] == "G":
nbG = nbRef
elif el[2] == "c" or el[2] == "C":
nbC = nbRef
elif el[2] == "t" or el[2] == "T":
nbT = nbRef
if el[3] == "A":
nbCns = nbA
elif el[3] == "G":
nbCns = nbG
elif el[3] == "C":
nbCns = nbC
elif el[3] == "T":
nbCns = nbT
else:
nbCns = "-"
listNb = [nbA, nbC, nbG, nbT]
resMaj = max(listNb)
ratio = nbRef / cov
ratio2 = resMaj / cov
if ratio2 != 1:
of.write("%s\t%s\t%s\t%s\t%s\t%s\t%.3f\t%s\t%s\t%s\t%s\t%.0f\t%.3f\n" % (
el[0], el[1], el[2].upper(), el[3], nbCns, el[5], ratio, nbA, nbC, nbG, nbT, cov, ratio2))
line = fM.readline()
of.close()
fM.close()
def fromVarfilter2tsvLike(ficVar):
ficSnp = traitementSamtools.decomposeVarfilter(ficVar)
#ficSnp = ficVar
#ficSnp = ficVar.replace("varfilter","SNP")
ficTsv = "%s.tsv" % ficSnp
of = open(ficTsv,"w")
fM = open(ficSnp,"r")
line = fM.readline()
of.write("Chromosome\tposition\tReference\tResidue\tnb Residue(if A,C,T orG)\tQuality score?\t(nb ref)/cov\tnb A\tnb C\tnb G\tnb T\tcov\n")
while line:
el = line.split("\t")
# ne tient pas compte des indels etc dans la ligne
#print "---%s---" % el
while string.find(el[8],"^") != -1: # si dedans
el[8] = string.replace(el[8],el[8][string.find(el[8],"^"):string.find(el[8],"^")+2],"") #on vire les infos ^et 2 par rien
lfin=removePatternFromLine("[\+|-]([0-9]+)([ACGTNacgtn]+)",el[8])
lfin=lfin.upper()
nbA=lfin.count("A")
nbC=lfin.count("C")
nbG=lfin.count("G")
nbT=lfin.count("T")
cov = string.atof(el[7])
nbRef = el[8].count(".") + el[8].count(",")
if el[2] == "a" or el[2] == "A":
nbA = nbRef
elif el[2] == "g" or el[2] == "G":
nbG = nbRef
elif el[2] == "c" or el[2] == "C":
nbC = nbRef
elif el[2] == "t" or el[2] == "T":
nbT = nbRef
if el[3] == "A":
nbCns = nbA
elif el[3] == "G":
nbCns = nbG
elif el[3] == "C":
nbCns = nbC
elif el[3] == "T":
nbCns = nbT
else :
nbCns = "-"
ratio = nbRef / cov
of.write("%s\t%s\t%s\t%s\t%s\t%s\t%.3f\t%s\t%s\t%s\t%s\t%.0f\n" % (el[0],el[1],el[2].upper(),el[3],nbCns,el[5],ratio,nbA,nbC,nbG,nbT,cov))
line = fM.readline()
of.close()
fM.close()
return ficTsv
def fromVarfilter2tsvLikeCyrielle(ficVar):
"""
compte le nombre de A,C,G,T par Reads pour un SNP
input: fichier pileup.SNP
"""
ficSnp = traitementSamtools.decomposeVarfilter(ficVar)
ficTsv = "%s.bestFilter.tsv" % ficSnp
of = open(ficTsv,"w")
fM = open(ficSnp,"r")
line = fM.readline()
of.write("Chromosome\tposition\tReference\tResidue\tnb Residue(if A,C,T orG)\tQuality score?\t(nb ref)/cov\tnb A\tnb C\tnb G\tnb T\tcov\t(nb max represented)/cov\n")
while line:
el = line.split("\t")
# ne tient pas compte des indels etc dans la ligne
#print "---%s---" % el
while string.find(el[8],"^") != -1: # si dedans
el[8] = string.replace(el[8],el[8][string.find(el[8],"^"):string.find(el[8],"^")+2],"") #on vire les infos ^et 2 par rien
lfin=removePatternFromLine("[\+|-]([0-9]+)([ACGTNacgtn]+)",el[8])
lfin=lfin.upper()
nbA=lfin.count("A")
nbC=lfin.count("C")
nbG=lfin.count("G")
nbT=lfin.count("T")
cov = string.atof(el[7])
nbRef = lfin.count(".") + lfin.count(",")
el2=el[2].upper()
if el2 == "A":
nbA = nbRef
elif el2 == "G":
nbG = nbRef
elif el2 == "C":
nbC = nbRef
elif el2 == "T":
nbT = nbRef
if el[3] == "A":
nbCns = nbA
elif el[3] == "G":
nbCns = nbG
elif el[3] == "C":
nbCns = nbC
elif el[3] == "T":
nbCns = nbT
else :
nbCns = "-"
listNb = [nbA,nbC,nbG,nbT]
resMaj = max(listNb)
ratio = nbRef / cov
ratio2 = resMaj / cov
if ratio2 <= 0.95:
of.write("%s\t%s\t%s\t%s\t%s\t%s\t%.3f\t%s\t%s\t%s\t%s\t%.0f\t%.3f\n" % (el[0],el[1],el[2].upper(),el[3],nbCns,el[5],ratio,nbA,nbC,nbG,nbT,cov,ratio2))
line = fM.readline()
of.close()
fM.close()
return ficTsv
