Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 8:d5badf9de1b0 draft

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planemo upload commit 968cd5b4f78f0a1da86fc3bc29f8159f86e199aa-dirty
author proteore
date Tue, 12 Mar 2019 05:43:54 -0400
parents f281a1eb83d6
children cdd29444e0af
comparison
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7:77db6c42a212 8:d5badf9de1b0
492 492
493 ####################################################################################################### 493 #######################################################################################################
494 # 5. nextprot (add protein features) 494 # 5. nextprot (add protein features)
495 ####################################################################################################### 495 #######################################################################################################
496 496
497 def Build_nextprot_ref_file(target_directory): 497 def Build_nextprot_ref_file(data_manager_dict,target_directory):
498 nextprot_ids_file = "nextprot_ac_list_all.txt" 498 nextprot_ids_file = "nextprot_ac_list_all.txt"
499 ids = id_list_from_nextprot_ftp(nextprot_ids_file,target_directory) 499 ids = id_list_from_nextprot_ftp(nextprot_ids_file,target_directory)
500 500
501 nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"]] 501 nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"]]
502 for id in ids : 502 for id in ids :
633 try: 633 try:
634 database=args.database 634 database=args.database
635 except NameError: 635 except NameError:
636 database=None 636 database=None
637 if database is not None : 637 if database is not None :
638 Build_nextprot_ref_file(target_directory) 638 Build_nextprot_ref_file(data_manager_dict,target_directory)
639 639
640 #save info to json file 640 #save info to json file
641 filename = args.output 641 filename = args.output
642 open(filename, 'wb').write(to_json_string(data_manager_dict)) 642 open(filename, 'wb').write(to_json_string(data_manager_dict))
643 643