Mercurial > repos > proteore > proteore_data_manager
comparison data_manager/resource_building.py @ 53:bb552aa4b9ac draft
"planemo upload commit 59b014e9f6e2d668cbd7c4844b10db3d59baefd8-dirty"
| author | proteore |
|---|---|
| date | Fri, 05 Jun 2020 13:49:53 +0000 |
| parents | 55b12ec24a9f |
| children | 109fc5236204 |
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| 52:93bb1170280d | 53:bb552aa4b9ac |
|---|---|
| 279 ftp.retrbinary("RETR " + file, open(path, 'wb').write) | 279 ftp.retrbinary("RETR " + file, open(path, 'wb').write) |
| 280 ftp.quit() | 280 ftp.quit() |
| 281 return (path) | 281 return (path) |
| 282 | 282 |
| 283 def id_list_from_nextprot_ftp(file,target_directory) : | 283 def id_list_from_nextprot_ftp(file,target_directory) : |
| 284 ftp_dir = "pub/current_release/ac_lists/" | |
| 284 path = os.path.join(target_directory, file) | 285 path = os.path.join(target_directory, file) |
| 285 ftp = ftplib.FTP("ftp.nextprot.org") | 286 ftp = ftplib.FTP("ftp.nextprot.org") |
| 286 ftp.login("anonymous", "anonymous") | 287 ftp.login("anonymous", "anonymous") |
| 287 ftp.cwd("pub/current_release/ac_lists/") | 288 ftp.cwd(ftp_dir) |
| 288 r = StringIO() | 289 ftp.retrbinary("RETR " + file, open(path, 'wb').write) |
| 289 ftp.retrlines("RETR " + file, lambda line: r.write(line + '\n')) | |
| 290 ftp.quit() | 290 ftp.quit() |
| 291 r.seek(0) | 291 with open(path,'r') as nextprot_ids : |
| 292 ids = r.readlines() | 292 nextprot_ids = nextprot_ids.read().splitlines() |
| 293 ids = [id.strip('\n') for id in ids if id != ''] | 293 return (nextprot_ids) |
| 294 return (ids) | |
| 295 | 294 |
| 296 #return '' if there's no value in a dictionary, avoid error | 295 #return '' if there's no value in a dictionary, avoid error |
| 297 def access_dictionary (dico,key1,key2) : | 296 def access_dictionary (dico,key1,key2) : |
| 298 if key1 in dico : | 297 if key1 in dico : |
| 299 if key2 in dico[key1] : | 298 if key2 in dico[key1] : |