Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 1:f3507260b30f draft

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planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c
author proteore
date Tue, 16 Apr 2019 07:46:59 -0400
parents 9e31ea9fc7ea
children 9ec42cb35abd
comparison
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0:9e31ea9fc7ea 1:f3507260b30f
537 if len(all_diseases) > 0 : all_diseases = ";".join(all_diseases) 537 if len(all_diseases) > 0 : all_diseases = ";".join(all_diseases)
538 else : all_diseases="NA" 538 else : all_diseases="NA"
539 else : 539 else :
540 all_diseases="NA" 540 all_diseases="NA"
541 541
542 #get all tm domain 542 #get all tm domain
543 nb_domains = 0 543 nb_domains = 0
544 if "domain" in data['entry']['annotationsByCategory'].keys(): 544 if "transmembrane-region" in data['entry']['annotationsByCategory'].keys():
545 tm_domains = data['entry']['annotationsByCategory']["domain"] 545 tm_domains = data['entry']['annotationsByCategory']["transmembrane-region"]
546 for tm_domain in tm_domains : 546 all_tm_domains = set()
547 if "properties" in tm_domain.keys() and tm_domain['properties']!=[]: 547 for tm in tm_domains :
548 domains = tm_domains["properties"] 548 all_tm_domains.add(tm['cvTermName'])
549 for domain in domains : 549 nb_domains+=1
550 if domain["name"]=="region structure" and domain["value"]=="Helical" : 550 print "nb domains ++"
551 nb_domains+=1 551 print (nb_domains)
552 552
553 553 nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])
554 nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])
555 554
556 output_file = 'nextprot_ref_'+ time.strftime("%d-%m-%Y") + ".tsv" 555 output_file = 'nextprot_ref_'+ time.strftime("%d-%m-%Y") + ".tsv"
557 path = os.path.join(target_directory,output_file) 556 path = os.path.join(target_directory,output_file)
558 name = "neXtProt release "+time.strftime("%d-%m-%Y") 557 name = "neXtProt release "+time.strftime("%d-%m-%Y")
559 id = "nextprot_ref_"+time.strftime("%d-%m-%Y") 558 id = "nextprot_ref_"+time.strftime("%d-%m-%Y")