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Commit 1d0b217a authored by Simon Gosset's avatar Simon Gosset
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changement regex identification transposons

parent 510a963b
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inst/biogridPy.py
View file @ 1d0b217a
......@@ -6,15 +6,15 @@ import re
### python biogridPy.py uniprotfile sortie putative
try:
uniprot = sys.argv[sys.argv.index("biogridPy.py")+1]
uniprot = sys.argv[sys.argv.index("biogridPy.py")+1]
except:
print ("ERROR: please, enter uniprot file")
sys.exit()
print ("ERROR: please, enter uniprot file")
sys.exit()
try:
thesaurus = sys.argv[sys.argv.index("biogridPy.py")+2]
thesaurus = sys.argv[sys.argv.index("biogridPy.py")+2]
except:
sys.exit()
sys.exit()
### Recuperation des donnees
......@@ -33,98 +33,101 @@ Transposon = "FALSE"
for i in fichier :
i = i.strip("\n")
# Recuperation de l'identifiant uniprot de la proteine
if i[0:2] == "AC" :
if ID == "NA" :
ID = re.search(r"(AC)(\s)*(?P<ac>\w+)(;)", i)
if ID is not None:
ID = ID.group('ac')
ID = str(ID)
else :
ID = 'NA'
# Recuperation du nom principal de la proteine
if i[0:2] == "ID" :
NameProt = re.search(r"(ID)(\s)*(?P<id>\w+)(_)", i)
if NameProt is not None:
NameProt = NameProt.group('id')
NameProt = str(NameProt)
else :
NameProt = 'NA'
# Recuperation du nom du gene
if i[0:2] == "GN" :
if Name == "NA" :
ligneName = i.split(";")
for k in ligneName :
k = k.replace(" ", "")
NAME = re.search(r"(Name=)(?P<id>\S+)$", k)
if NAME is not None:
Name = NAME.group('id')
Name = str(Name)
sup = re.search(r"({)(?P<SUP>\S+)$", Name)
if sup is not None :
sup = sup.group('SUP')
sup = '{' + sup
Name = Name.replace(sup, "")
else :
NAME = 'NA'
# Recuperation de l'identifiant biogrid
elif i[0:12] == "DR GeneID;" :
Biogrid = re.search(r"(DR GeneID;)(\s)*(?P<bg>\w+)(;)", i)
if Biogrid is not None:
Biogrid = Biogrid.group('bg')
Biogrid = str(Biogrid)
BIOGRID.append(Biogrid)
else :
Biogrid = 'NA'
# Recuperation de l'identifiant biogrid : id alternatif
elif i[0:12] == "DR BioGrid;" :
Biogrid = re.search(r"(DR GeneID;)(\s)*(?P<bg>\w+)(;)", i)
if Biogrid is not None:
Biogrid = Biogrid.group('bg')
Biogrid = str(Biogrid)
BIOGRID.append(Biogrid)
else :
Biogrid = 'NA'
# Recuperation du RecName : Putative, Transposon
elif i[0:13] == "DE RecName:" :
if Putative == "FALSE" :
Putative = re.search(r"(DE RecName:)(\s)*(Full=Putative)(.)*", i)
if Putative is not None:
Putative = "TRUE"
else :
Putative = "FALSE"
if Transposon == "FALSE" :
Transposon = re.search(r"(DE RecName:)(\s)*(Full=Transposon)(.)*", i)
if Transposon is not None:
Transposon = "TRUE"
else :
Transposon = "FALSE"
# A la fin de chaque bloc (chaque proteine) les donnees sont rassemblees sur une meme ligne
elif i[0:2] == "//" :
b = len(BIOGRID)
if b > 0 :
Biogrid = ''
for B in range(0,b) :
Biogrid = str(BIOGRID[B]) + ';'
ligne = ID + "\t" + Biogrid + "\t" + NameProt + "\t" + Name + "\t" + Putative + "\t" + Transposon
donnees.append(ligne)
ligne = 'NA'
ID = 'NA'
NameProt = 'NA'
Name = 'NA'
Biogrid = 'NA'
BIOGRID = []
Putative = "FALSE"
Transposon = "FALSE"
i = i.strip("\n")
# Recuperation de l'identifiant uniprot de la proteine
if i[0:2] == "AC" :
if ID == "NA" :
ID = re.search(r"(AC)(\s)*(?P<ac>\w+)(;)", i)
if ID is not None:
ID = ID.group('ac')
ID = str(ID)
else :
ID = 'NA'
# Recuperation du nom principal de la proteine
if i[0:2] == "ID" :
NameProt = re.search(r"(ID)(\s)*(?P<id>\w+)(_)", i)
if NameProt is not None:
NameProt = NameProt.group('id')
NameProt = str(NameProt)
else :
NameProt = 'NA'
# Recuperation du nom du gene
if i[0:2] == "GN" :
if Name == "NA" :
ligneName = i.split(";")
for k in ligneName :
k = k.replace(" ", "")
NAME = re.search(r"(Name=)(?P<id>\S+)$", k)
if NAME is not None:
Name = NAME.group('id')
Name = str(Name)
sup = re.search(r"({)(?P<SUP>\S+)$", Name)
if sup is not None :
sup = sup.group('SUP')
sup = '{' + sup
Name = Name.replace(sup, "")
else :
NAME = 'NA'
# Recuperation de l'identifiant biogrid
elif i[0:12] == "DR GeneID;" :
Biogrid = re.search(r"(DR GeneID;)(\s)*(?P<bg>\w+)(;)", i)
if Biogrid is not None:
Biogrid = Biogrid.group('bg')
Biogrid = str(Biogrid)
BIOGRID.append(Biogrid)
else :
Biogrid = 'NA'
# Recuperation de l'identifiant biogrid : id alternatif
elif i[0:13] == "DR BioGRID;" :
# print(i)
# Biogrid = re.search(r"(DR BioGrid;)(\s)*(?P<bg>\w+)(;)", i)
Biogrid = i.split(sep=";")[1]
Biogrid = Biogrid.strip()
if Biogrid is not None:
# Biogrid = Biogrid.group('bg')
Biogrid = str(Biogrid)
BIOGRID.append(Biogrid)
else :
Biogrid = 'NA'
# Recuperation du RecName : Putative, Transposon
elif i[0:13] == "DE RecName:" :
if Putative == "FALSE" :
Putative = re.search(r"(DE RecName:)(\s)*(Full=Putative)(.)*", i)
if Putative is not None:
Putative = "TRUE"
else :
Putative = "FALSE"
if Transposon == "FALSE" :
Transposon = re.search(r"(DE RecName:)(\s)*(Full=)(.)*([Tt]ransposon)(.)*", i)
if Transposon is not None:
Transposon = "TRUE"
else :
Transposon = "FALSE"
# A la fin de chaque bloc (chaque proteine) les donnees sont rassemblees sur une meme ligne
elif i[0:2] == "//" :
b = len(BIOGRID)
if b > 0 :
Biogrid = ''
for B in range(0,b) :
Biogrid = str(BIOGRID[B]) + ';'
ligne = ID + "\t" + Biogrid + "\t" + NameProt + "\t" + Name + "\t" + Putative + "\t" + Transposon
donnees.append(ligne)
ligne = 'NA'
ID = 'NA'
NameProt = 'NA'
Name = 'NA'
Biogrid = 'NA'
BIOGRID = []
Putative = "FALSE"
Transposon = "FALSE"
fichier.close()
......@@ -136,8 +139,8 @@ sortie.write("Uniprot-ID\tBiogrid-ID\tProtein-Name\tGene-Name\tPutative\tTranspo
N = len(donnees)
for i in range(0,N) :
sortie.write("\n")
sortie.write(donnees[i])
sortie.write("\n")
sortie.write(donnees[i])
sortie.close()
inst/thesaurusPy.py
View file @ 1d0b217a
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