Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 9:cdd29444e0af draft

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planemo upload commit 71363136045353f422ff98219c1eb84f6fc6193a-dirty
author proteore
date Tue, 12 Mar 2019 06:40:37 -0400
parents d5badf9de1b0
children ac2cd728c40e
comparison
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8:d5badf9de1b0 9:cdd29444e0af
426 r = s.get('http://proteincomplexes.org/static/downloads/nodeTable.txt') 426 r = s.get('http://proteincomplexes.org/static/downloads/nodeTable.txt')
427 r = r.content.decode('utf-8') 427 r = r.content.decode('utf-8')
428 humap_nodes = csv.reader(r.splitlines(), delimiter=',') 428 humap_nodes = csv.reader(r.splitlines(), delimiter=',')
429 429
430 dico_geneid_to_gene_name={} 430 dico_geneid_to_gene_name={}
431 dico_protein_name={}
431 for line in humap_nodes : 432 for line in humap_nodes :
432 if check_entrez_geneid(line[4]): 433 if check_entrez_geneid(line[4]):
433 if line[4] not in dico_geneid_to_gene_name: 434 if line[4] not in dico_geneid_to_gene_name:
434 dico_geneid_to_gene_name[line[4]]=line[3] 435 dico_geneid_to_gene_name[line[4]]=line[3]
435 436 if line[4] not in dico_protein_name:
437 dico_protein_name[line[4]]=line[5]
438
436 with requests.Session() as s: 439 with requests.Session() as s:
437 r = s.get('http://proteincomplexes.org/static/downloads/pairsWprob.txt') 440 r = s.get('http://proteincomplexes.org/static/downloads/pairsWprob.txt')
438 r = r.content.decode('utf-8') 441 r = r.content.decode('utf-8')
439 humap = csv.reader(r.splitlines(), delimiter='\t') 442 humap = csv.reader(r.splitlines(), delimiter='\t')
440 443
475 478
476 dico={} 479 dico={}
477 dico['network']=dico_network 480 dico['network']=dico_network
478 dico['nodes']=dico_nodes 481 dico['nodes']=dico_nodes
479 dico['gene_name']=dico_geneid_to_gene_name 482 dico['gene_name']=dico_geneid_to_gene_name
483 dico['protein_name']=dico_protein_name
480 484
481 #writing output 485 #writing output
482 output_file = species+'_'+interactome+'_'+ time.strftime("%d-%m-%Y") + ".json" 486 output_file = species+'_'+interactome+'_'+ time.strftime("%d-%m-%Y") + ".json"
483 path = os.path.join(target_directory,output_file) 487 path = os.path.join(target_directory,output_file)
484 name = species+" ("+species_dict[species]+") "+time.strftime("%d/%m/%Y") 488 name = species+" ("+species_dict[species]+") "+time.strftime("%d/%m/%Y")