Mercurial > repos > jbrayet > rsat
comparison peakMotifs_wrapper.py @ 50:a21c2253cafc draft
Uploaded
| author | jbrayet |
|---|---|
| date | Tue, 29 Sep 2015 07:37:29 -0400 |
| parents | dce9495ac542 |
| children | 9e193aa2b9d2 |
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| 49:94b3643ce679 | 50:a21c2253cafc |
|---|---|
| 195 variable = "" | 195 variable = "" |
| 196 return variable | 196 return variable |
| 197 | 197 |
| 198 | 198 |
| 199 ###########################################################' | 199 ###########################################################' |
| 200 ## Function to recup results | 200 ## Functions to recup results |
| 201 | 201 |
| 202 def buildZipUrl(algoResults): | 202 def buildZipUrl(algoResults): |
| 203 """ | 203 """ |
| 204 Recup results give by RSAT server. | 204 Recup results give by RSAT server. |
| 205 algoResults -> result give by RSAT server | 205 algoResults -> response gave by RSAT server |
| 206 """ | 206 """ |
| 207 | 207 |
| 208 recupResult = str(algoResults) | 208 recupResult = str(algoResults) |
| 209 tabResults=recupResult.split("\n") | 209 tabResults=recupResult.split("\n") |
| 210 urlZip = tabResults[4].replace("\t","") | 210 urlZip = tabResults[4].replace("\t","") |
| 211 | 211 |
| 212 return urlZip | 212 return urlZip |
| 213 | 213 |
| 214 def recupRSATResult(urlResult,nameFile): | |
| 215 | |
| 216 """ | |
| 217 Recup results give by RSAT server. | |
| 218 urlResult -> URL gave by RSAT server | |
| 219 nameFile -> name of zip file in Galaxy path | |
| 220 """ | |
| 221 | |
| 222 ###########################################################' | |
| 223 ## Download RSAT results | |
| 224 urllib.urlretrieve(urlResult, nameFile) | |
| 225 #except IOError: | |
| 226 #logFile.write("\nResult URL is false") | |
| 227 #Logger.error("Result URL is false") | |
| 228 #logFile.write("\n"+nameFile+"\n") | |
| 229 | |
| 230 ###########################################################' | |
| 231 ## Decompress results | |
| 232 #try: | |
| 233 zfile = zipfile.ZipFile(nameFile, 'r') | |
| 234 #except IOError: | |
| 235 #logFile.write("No zip file") | |
| 236 #Logger.error("No zip file") | |
| 237 | |
| 238 tempflag = 0 | |
| 239 folderName ="" | |
| 240 | |
| 241 for i in zfile.namelist(): ## On parcourt l'ensemble des fichiers de l'archive | |
| 242 | |
| 243 #logFile.write(i+"\n") | |
| 244 ############################### | |
| 245 if tempflag ==0: | |
| 246 folderName = i | |
| 247 | |
| 248 tempflag = 1 | |
| 249 ############################### | |
| 250 | |
| 251 if i.endswith('/'): ## S'il s'agit d'un repertoire, on se contente de creer le dossier | |
| 252 os.makedirs(i) | |
| 253 else: | |
| 254 data = zfile.read(i) ## lecture du fichier compresse | |
| 255 fp = open(i, "wb") ## creation en local du nouveau fichier | |
| 256 fp.write(data) ## ajout des donnees du fichier compresse dans le fichier local | |
| 257 fp.close() | |
| 258 zfile.close() | |
| 259 | |
| 260 return folderName | |
| 214 | 261 |
| 215 ## Tested with python 2.6.6 | 262 ## Tested with python 2.6.6 |
| 216 peakMotifsVersion = '0.1 - 30/01/2015' | 263 peakMotifsVersion = '2.0 - 30/01/2015' |
| 217 | 264 |
| 218 ###########################################################' | 265 ###########################################################' |
| 219 # server dictionary | 266 # server dictionary |
| 220 serverDict = { | 267 serverDict = { |
| 221 | 268 |
| 415 while urllib.urlopen(urlResult).getcode() != 200: | 462 while urllib.urlopen(urlResult).getcode() != 200: |
| 416 #logFile.write(str(urllib.urlopen(urlResult).getcode())+"\n") | 463 #logFile.write(str(urllib.urlopen(urlResult).getcode())+"\n") |
| 417 time.sleep(5) | 464 time.sleep(5) |
| 418 | 465 |
| 419 #logFile.write(str(nameFile)+"\n") | 466 #logFile.write(str(nameFile)+"\n") |
| 420 | 467 #time.sleep(5) |
| 421 #while urllib.urlretrieve(urlResult, nameFile) | 468 #while urllib.urlretrieve(urlResult, nameFile) |
| 422 #try: | 469 #try: |
| 423 ###########################################################' | 470 |
| 424 ## Download RSAT results | 471 folderName=recupRSATResult(urlResult,nameFile) |
| 425 urllib.urlretrieve(urlResult, nameFile) | 472 |
| 426 #except IOError: | 473 while(not(os.path.exists(folderName+"peak-motifs_synthesis.html"))): |
| 427 #logFile.write("\nResult URL is false") | 474 os.popen("rm -rf "+folderName) |
| 428 #Logger.error("Result URL is false") | 475 recupRSATResult(urlResult,nameFile) |
| 429 | |
| 430 | |
| 431 #logFile.write("\n"+nameFile+"\n") | |
| 432 | |
| 433 ###########################################################' | |
| 434 ## Decompress results | |
| 435 #try: | |
| 436 zfile = zipfile.ZipFile(nameFile, 'r') | |
| 437 #except IOError: | |
| 438 #logFile.write("No zip file") | |
| 439 #Logger.error("No zip file") | |
| 440 | |
| 441 tempflag = 0 | |
| 442 folderName ="" | |
| 443 | |
| 444 for i in zfile.namelist(): ## On parcourt l'ensemble des fichiers de l'archive | |
| 445 | |
| 446 #logFile.write(i+"\n") | |
| 447 ############################### | |
| 448 if tempflag ==0: | |
| 449 folderName = i | |
| 450 | |
| 451 tempflag = 1 | |
| 452 ############################### | |
| 453 | |
| 454 if i.endswith('/'): ## S'il s'agit d'un repertoire, on se contente de creer le dossier | |
| 455 os.makedirs(i) | |
| 456 else: | |
| 457 data = zfile.read(i) ## lecture du fichier compresse | |
| 458 fp = open(i, "wb") ## creation en local du nouveau fichier | |
| 459 fp.write(data) ## ajout des donnees du fichier compresse dans le fichier local | |
| 460 fp.close() | |
| 461 zfile.close() | |
| 462 | 476 |
| 463 #logFile.write("\n"+folderName+"\n") | 477 #logFile.write("\n"+folderName+"\n") |
| 464 #logFile.write("\n"+outGalaxyValue+"\n") | 478 #logFile.write("\n"+outGalaxyValue+"\n") |
| 465 | 479 |
| 466 os.popen("cp "+folderName+"peak-motifs_synthesis.html "+outGalaxyValue) | 480 os.popen("cp "+folderName+"peak-motifs_synthesis.html "+outGalaxyValue) |