Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 3:18d3b1ea7a18 draft

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planemo upload commit c6e1fd1f68e81ce9eea6ad66adee21070f2893ef-dirty
author proteore
date Wed, 06 Mar 2019 09:50:27 -0500
parents 2e34ee6d2d37
children ce01295cd601
comparison
equal deleted inserted replaced
2:2e34ee6d2d37 3:18d3b1ea7a18
229 229
230 name_dict={"Human" : "Homo sapiens", "Mouse" : "Mus musculus", "Rat" : "Rattus norvegicus"} 230 name_dict={"Human" : "Homo sapiens", "Mouse" : "Mus musculus", "Rat" : "Rattus norvegicus"}
231 name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")" 231 name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")"
232 id = species+"_id_mapping_"+ time.strftime("%d-%m-%Y") 232 id = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
233 233
234 data_table_entry = dict(id=id, name = name, value = species, path = path) 234 data_table_entry = dict(id=id, name = name, species = species, value = path)
235 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping_"+species) 235 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping_"+species)
236 236
237 def download_from_uniprot_ftp(file,target_directory) : 237 def download_from_uniprot_ftp(file,target_directory) :
238 ftp_dir = "pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/" 238 ftp_dir = "pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
239 path = os.path.join(target_directory, file) 239 path = os.path.join(target_directory, file)