Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 14:3f9ba522bfe8 draft

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planemo upload commit 272d182247f4fa55a928ec8cdcb83eab50c7f6ef
author proteore
date Wed, 17 Apr 2019 10:23:25 -0400
parents 098693479a9d
children 5f39d3ef5fe3
comparison
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13:098693479a9d 14:3f9ba522bfe8
512 writer = csv.writer(output,delimiter="\t") 512 writer = csv.writer(output,delimiter="\t")
513 513
514 514
515 515
516 nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"]] 516 nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"]]
517 writer.writerows(nextprot_file)
518
517 for id in ids : 519 for id in ids :
518 #print (id) 520 #print (id)
519 query="https://api.nextprot.org/entry/"+id+".json" 521 query="https://api.nextprot.org/entry/"+id+".json"
520 resp = requests.get(url=query) 522 resp = requests.get(url=query)
521 data = resp.json() 523 data = resp.json()
558 for tm in tm_domains : 560 for tm in tm_domains :
559 all_tm_domains.add(tm['cvTermName']) 561 all_tm_domains.add(tm['cvTermName'])
560 nb_domains+=1 562 nb_domains+=1
561 # print "nb domains ++" 563 # print "nb domains ++"
562 # print (nb_domains) 564 # print (nb_domains)
563 565 nextprot_file.clear()
564 nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence]) 566 nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])
565 writer.writerows(nextprot_file) 567 writer.writerows(nextprot_file)
566 568
567 data_table_entry = dict(id=id, name = name, value = path) 569 data_table_entry = dict(id=id, name = name, value = path)
568 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_nextprot_ref") 570 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_nextprot_ref")