comparison data_manager/resource_building.py @ 22:778cc97cb115 draft

planemo upload commit e2e4ac8c2c4dc5675d4c415ff192a925ca5e6b98-dirty
author dchristiany
date Thu, 17 Jan 2019 08:17:01 -0500
parents 0a79066992fc
children b2584295ef44
comparison
equal deleted inserted replaced
21:0a79066992fc 22:778cc97cb115
299 tab_file = csv.reader(handle,delimiter="\t") 299 tab_file = csv.reader(handle,delimiter="\t")
300 dico_network = {} 300 dico_network = {}
301 GeneID_index=1 301 GeneID_index=1
302 network_cols=[1,2,7,8,11,12,18,20] 302 network_cols=[1,2,7,8,11,12,18,20]
303 for line in tab_file : 303 for line in tab_file :
304 dico_network[line[GeneID_index]]=[line[i] for i in network_cols] 304 if line[GeneID_index] not in dico_network:
305 dico_network[line[GeneID_index]]=[[line[i] for i in network_cols]]
306 else:
307 dico_network[line[GeneID_index]].append([line[i] for i in network_cols])
305 308
306 #delete tmp_BioGRID directory 309 #delete tmp_BioGRID directory
307 os.remove("BioGRID.zip") 310 os.remove("BioGRID.zip")
308 shutil.rmtree("tmp_BioGRID", ignore_errors=True) 311 shutil.rmtree("tmp_BioGRID", ignore_errors=True)
309 312
338 dico_network["UniProt-AC"]={} 341 dico_network["UniProt-AC"]={}
339 network_uniprot_cols=[2,3,4,5,8] 342 network_uniprot_cols=[2,3,4,5,8]
340 dico_GeneID_to_UniProt = {} 343 dico_GeneID_to_UniProt = {}
341 dico_nodes = {} 344 dico_nodes = {}
342 for line in bioplex : 345 for line in bioplex :
343 dico_network["GeneID"][line[0]]=[line[i] for i in network_geneid_cols] 346 if line[0] not in dico_network["GeneID"]:
344 dico_network["UniProt-AC"][line[2]]=[line[i] for i in network_uniprot_cols] 347 dico_network["GeneID"][line[0]]=[[line[i] for i in network_geneid_cols]]
348 else :
349 dico_network["GeneID"][line[0]].append([line[i] for i in network_geneid_cols])
350 if line[1] not in dico_network["UniProt-AC"]:
351 dico_network["UniProt-AC"][line[2]]=[[line[i] for i in network_uniprot_cols]]
352 else:
353 dico_network["UniProt-AC"][line[2]].append([line[i] for i in network_uniprot_cols])
345 dico_GeneID_to_UniProt[line[0]]=line[2] 354 dico_GeneID_to_UniProt[line[0]]=line[2]
346 355
347 r = requests.get("https://reactome.org/download/current/UniProt2Reactome.txt") 356 r = requests.get("https://reactome.org/download/current/UniProt2Reactome.txt")
348 r.encoding ="utf-8" 357 r.encoding ="utf-8"
349 tab_file = csv.reader(r.content.splitlines(), delimiter='\t') 358 tab_file = csv.reader(r.content.splitlines(), delimiter='\t')