Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 65:64b2d53be08b draft default tip

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"planemo upload commit b218f949aa7a17b1e75a35946a3a19194bf168f3-dirty"
author proteore
date Fri, 31 Jul 2020 14:02:26 +0000
parents 570519e1d968
children
comparison
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64:570519e1d968 65:64b2d53be08b
555 release_id = "nextprot_ref_"+time.strftime("%d-%m-%Y") 555 release_id = "nextprot_ref_"+time.strftime("%d-%m-%Y")
556 556
557 output = open('test.csv', 'w') 557 output = open('test.csv', 'w')
558 writer = csv.writer(output,delimiter="\t") 558 writer = csv.writer(output,delimiter="\t")
559 559
560 nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence","ProteinName","Function","PostTranslationalModifications","ProteinFamily","Pathway"]] 560 nextprot_file=[["NextprotID","ProteinName","SeqLength","MW","IsoPoint","TMDomains","SubcellLocations","Diseases","Function","PostTranslationalModifications","ProteinFamily","Pathway","ProteinExistence","Chr"]]
561 writer.writerows(nextprot_file) 561 writer.writerows(nextprot_file)
562 562
563 for id in ids : 563 for id in ids :
564 query="https://api.nextprot.org/entry/"+id+".json" 564 query="https://api.nextprot.org/entry/"+id+".json"
565 try: 565 try:
642 nb_domains+=1 642 nb_domains+=1
643 #print "nb domains ++" 643 #print "nb domains ++"
644 #print (nb_domains) 644 #print (nb_domains)
645 645
646 nextprot_file[:] = [] 646 nextprot_file[:] = []
647 nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence,protein_name,function,post_trans_mod,protein_family,pathway]) 647 nextprot_file.append([id,protein_name,str(seq_length),mass_mol,iso_elec_point,str(nb_domains),all_subcell_locs,all_diseases,function,post_trans_mod,protein_family,pathway,protein_existence,chr_loc])
648 writer.writerows(nextprot_file) 648 writer.writerows(nextprot_file)
649 649
650 id = str(10000000000 - int(time.strftime("%Y%m%d"))) 650 id = str(10000000000 - int(time.strftime("%Y%m%d")))
651 651
652 data_table_entry = dict(id=id, release=release_id, name = name, value = path) 652 data_table_entry = dict(id=id, release=release_id, name = name, value = path)