Mercurial > repos > proteore > proteore_id_converter
comparison id_converter.py @ 21:6e65e1c78705 draft default tip
"planemo upload commit 540dd383c0617193db43bf11457011888751b022-dirty"
| author | proteore |
|---|---|
| date | Thu, 23 Jan 2020 08:43:51 -0500 |
| parents | 9d758344d36e |
| children |
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| 20:77a2cd4162b7 | 21:6e65e1c78705 |
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| 171 else : | 171 else : |
| 172 ids_dictionary[id][ids_dictionary_index[other_id_type]] |= set(line[other_id_type].replace("NA","").replace(" ","").split(";")) | 172 ids_dictionary[id][ids_dictionary_index[other_id_type]] |= set(line[other_id_type].replace("NA","").replace(" ","").split(";")) |
| 173 if len(ids_dictionary[id][ids_dictionary_index[other_id_type]]) > 1 and '' in ids_dictionary[id][ids_dictionary_index[other_id_type]] : | 173 if len(ids_dictionary[id][ids_dictionary_index[other_id_type]]) > 1 and '' in ids_dictionary[id][ids_dictionary_index[other_id_type]] : |
| 174 ids_dictionary[id][ids_dictionary_index[other_id_type]].remove('') | 174 ids_dictionary[id][ids_dictionary_index[other_id_type]].remove('') |
| 175 | 175 |
| 176 #print ("dictionary created") | |
| 177 | |
| 178 #Get file and/or ids from input | 176 #Get file and/or ids from input |
| 179 if args.input_type == "list" : | 177 if args.input_type == "list" : |
| 180 ids = get_input_ids_from_string(args.input) | 178 ids = get_input_ids_from_string(args.input) |
| 181 elif args.input_type == "file" : | 179 elif args.input_type == "file" : |
| 182 input_file, ids = get_input_ids_from_file(args.input,args.column_number,header) | 180 input_file, ids = get_input_ids_from_file(args.input,args.column_number,header) |
| 183 | 181 |
| 184 #print ("starting mapping") | |
| 185 | |
| 186 #Mapping ids | 182 #Mapping ids |
| 187 result_dict = map_to_dictionary(ids,ids_dictionary,args.id_type,target_ids) | 183 result_dict = map_to_dictionary(ids,ids_dictionary,args.id_type,target_ids) |
| 188 | 184 |
| 189 #print ("mapping done") | |
| 190 | |
| 191 #print ("creating output file") | |
| 192 #creating output file | 185 #creating output file |
| 193 with open(args.output,"w") as output : | 186 with open(args.output,"w") as output : |
| 194 writer = csv.writer(output,delimiter="\t") | 187 writer = csv.writer(output,delimiter="\t") |
| 195 #writer.writerows(output_file) | 188 #writer.writerows(output_file) |
| 196 | 189 |