Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 21:026177e4ff4b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty
author proteore
date Tue, 07 May 2019 10:17:48 -0400
parents 29cf75c83618
children 4296fb613d9d
comparison
equal deleted inserted replaced
20:29cf75c83618 21:026177e4ff4b
240 w = csv.writer(out,delimiter='\t') 240 w = csv.writer(out,delimiter='\t')
241 w.writerows(tab) 241 w.writerows(tab)
242 242
243 name_dict={"Human" : "Homo sapiens", "Mouse" : "Mus musculus", "Rat" : "Rattus norvegicus"} 243 name_dict={"Human" : "Homo sapiens", "Mouse" : "Mus musculus", "Rat" : "Rattus norvegicus"}
244 name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")" 244 name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")"
245 id = str(10000000000 - int(time.strftime("%d%m%Y"))) 245 release = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
246 246 id = str(10000000000 - int(time.strftime("%d%m%Y"))) #new ids must be inferior to previous id -> sort by <filter> in xml only in descending order
247 data_table_entry = dict(id=id, name = name, species = species, value = path) 247
248 data_table_entry = dict(id=id, release=release , name = name, species = species, value = path)
248 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping_"+species) 249 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping_"+species)
249 250
250 def download_from_uniprot_ftp(file,target_directory) : 251 def download_from_uniprot_ftp(file,target_directory) :
251 ftp_dir = "pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/" 252 ftp_dir = "pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
252 path = os.path.join(target_directory, file) 253 path = os.path.join(target_directory, file)