def get_uniprot_to_id(uniprot_file, uniprot_ids=None, only_min=True, key_function=int):
"""
uniprot_file = %(data_dir)s/uniprot/idmapping.tab or idmapping.tab.symbol or idmapping.tab.mouse
Can be used to convert to geneids (key_function=int) as well as symbols (key_function=len) depending on the input file
"""
uniprot_to_gene = parse_uniprot.get_uniprot_to_geneid(uniprot_file, uniprot_ids, only_min, key_function)
return uniprot_to_gene
def main():
mapping_file = "/home/emre/data/uniprot/idmapping.tab"
uniprot_to_geneid = parse_uniprot.get_uniprot_to_geneid(mapping_file, uniprot_ids=None)
file_name = "/home/emre/data/tissue/amigo_extracellular.tsv"
#file_name = "/home/emre/data/tissue/amigo_membrane.tsv"
geneid_to_localization = get_geneid_to_localization(file_name, mapping_file)
print geneid_to_localization["5594"] # MAPK1
return
def get_geneid_to_localization(file_name, mapping_file):
name_to_geneid = parse_uniprot.get_uniprot_to_geneid(mapping_file, uniprot_ids=None)
geneid_to_localization = {}
uniprots_unmatched = set()
for line in open(file_name):
words = line.strip("\n").split("\t")
uniprot, go, evidence = words[0], words[3], words[7]
idx = uniprot.find(":")
uniprot = uniprot[idx+1:]
#if evidence not in ("EXP", "IDA", "IPA", "IMP", "IGI", "IEP", "HDA"):
# continue
if uniprot in name_to_geneid:
geneid = name_to_geneid[uniprot]
else:
#print "Unmatched id", uniprot
if not uniprot.startswith("URS"):
uniprots_unmatched.add(uniprot)
continue
# Store evidence type as well
geneid_to_localization.setdefault(geneid, set()).add((go, evidence))
print "Unmatched:", len(uniprots_unmatched) #, ", ".join(sorted(uniprots_unmatched))
return geneid_to_localization
def get_uniprot_to_symbol(uniprot_symbol_file, uniprot_ids):
uniprot_to_geneid = parse_uniprot.get_uniprot_to_geneid(
uniprot_symbol_file, uniprot_ids, only_min=False)
return uniprot_to_geneid
def get_uniprot_to_geneid(uniprot_file, uniprot_ids):
uniprot_to_geneid = parse_uniprot.get_uniprot_to_geneid(
uniprot_file, uniprot_ids)
return uniprot_to_geneid
def get_uniprot_to_geneid(uniprot_file, uniprot_ids):
uniprot_to_geneid = parse_uniprot.get_uniprot_to_geneid(uniprot_file, uniprot_ids)
return uniprot_to_geneid
def get_uniprot_to_symbol(uniprot_symbol_file, uniprot_ids):
uniprot_to_geneid = parse_uniprot.get_uniprot_to_geneid(uniprot_symbol_file, uniprot_ids, only_min=False)
return uniprot_to_geneid
