Mercurial > repos > dchristiany > data_manager_proteore
comparison data_manager/resource_building.py @ 22:778cc97cb115 draft
planemo upload commit e2e4ac8c2c4dc5675d4c415ff192a925ca5e6b98-dirty
| author | dchristiany |
|---|---|
| date | Thu, 17 Jan 2019 08:17:01 -0500 |
| parents | 0a79066992fc |
| children | b2584295ef44 |
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| 21:0a79066992fc | 22:778cc97cb115 |
|---|---|
| 299 tab_file = csv.reader(handle,delimiter="\t") | 299 tab_file = csv.reader(handle,delimiter="\t") |
| 300 dico_network = {} | 300 dico_network = {} |
| 301 GeneID_index=1 | 301 GeneID_index=1 |
| 302 network_cols=[1,2,7,8,11,12,18,20] | 302 network_cols=[1,2,7,8,11,12,18,20] |
| 303 for line in tab_file : | 303 for line in tab_file : |
| 304 dico_network[line[GeneID_index]]=[line[i] for i in network_cols] | 304 if line[GeneID_index] not in dico_network: |
| 305 dico_network[line[GeneID_index]]=[[line[i] for i in network_cols]] | |
| 306 else: | |
| 307 dico_network[line[GeneID_index]].append([line[i] for i in network_cols]) | |
| 305 | 308 |
| 306 #delete tmp_BioGRID directory | 309 #delete tmp_BioGRID directory |
| 307 os.remove("BioGRID.zip") | 310 os.remove("BioGRID.zip") |
| 308 shutil.rmtree("tmp_BioGRID", ignore_errors=True) | 311 shutil.rmtree("tmp_BioGRID", ignore_errors=True) |
| 309 | 312 |
| 338 dico_network["UniProt-AC"]={} | 341 dico_network["UniProt-AC"]={} |
| 339 network_uniprot_cols=[2,3,4,5,8] | 342 network_uniprot_cols=[2,3,4,5,8] |
| 340 dico_GeneID_to_UniProt = {} | 343 dico_GeneID_to_UniProt = {} |
| 341 dico_nodes = {} | 344 dico_nodes = {} |
| 342 for line in bioplex : | 345 for line in bioplex : |
| 343 dico_network["GeneID"][line[0]]=[line[i] for i in network_geneid_cols] | 346 if line[0] not in dico_network["GeneID"]: |
| 344 dico_network["UniProt-AC"][line[2]]=[line[i] for i in network_uniprot_cols] | 347 dico_network["GeneID"][line[0]]=[[line[i] for i in network_geneid_cols]] |
| 348 else : | |
| 349 dico_network["GeneID"][line[0]].append([line[i] for i in network_geneid_cols]) | |
| 350 if line[1] not in dico_network["UniProt-AC"]: | |
| 351 dico_network["UniProt-AC"][line[2]]=[[line[i] for i in network_uniprot_cols]] | |
| 352 else: | |
| 353 dico_network["UniProt-AC"][line[2]].append([line[i] for i in network_uniprot_cols]) | |
| 345 dico_GeneID_to_UniProt[line[0]]=line[2] | 354 dico_GeneID_to_UniProt[line[0]]=line[2] |
| 346 | 355 |
| 347 r = requests.get("https://reactome.org/download/current/UniProt2Reactome.txt") | 356 r = requests.get("https://reactome.org/download/current/UniProt2Reactome.txt") |
| 348 r.encoding ="utf-8" | 357 r.encoding ="utf-8" |
| 349 tab_file = csv.reader(r.content.splitlines(), delimiter='\t') | 358 tab_file = csv.reader(r.content.splitlines(), delimiter='\t') |