Mercurial > repos > jbrayet > rsat
changeset 50:a21c2253cafc draft
Uploaded
| author | jbrayet |
|---|---|
| date | Tue, 29 Sep 2015 07:37:29 -0400 |
| parents | 94b3643ce679 |
| children | 9e193aa2b9d2 |
| files | peakMotifs_wrapper.py |
| diffstat | 1 files changed, 55 insertions(+), 41 deletions(-) [+] |
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--- a/peakMotifs_wrapper.py Tue Sep 29 07:37:17 2015 -0400 +++ b/peakMotifs_wrapper.py Tue Sep 29 07:37:29 2015 -0400 @@ -197,12 +197,12 @@ ###########################################################' -## Function to recup results +## Functions to recup results def buildZipUrl(algoResults): """ Recup results give by RSAT server. - algoResults -> result give by RSAT server + algoResults -> response gave by RSAT server """ recupResult = str(algoResults) @@ -211,9 +211,56 @@ return urlZip +def recupRSATResult(urlResult,nameFile): + + """ + Recup results give by RSAT server. + urlResult -> URL gave by RSAT server + nameFile -> name of zip file in Galaxy path + """ + + ###########################################################' + ## Download RSAT results + urllib.urlretrieve(urlResult, nameFile) + #except IOError: + #logFile.write("\nResult URL is false") + #Logger.error("Result URL is false") + #logFile.write("\n"+nameFile+"\n") + + ###########################################################' + ## Decompress results + #try: + zfile = zipfile.ZipFile(nameFile, 'r') + #except IOError: + #logFile.write("No zip file") + #Logger.error("No zip file") + + tempflag = 0 + folderName ="" + + for i in zfile.namelist(): ## On parcourt l'ensemble des fichiers de l'archive + + #logFile.write(i+"\n") + ############################### + if tempflag ==0: + folderName = i + + tempflag = 1 + ############################### + + if i.endswith('/'): ## S'il s'agit d'un repertoire, on se contente de creer le dossier + os.makedirs(i) + else: + data = zfile.read(i) ## lecture du fichier compresse + fp = open(i, "wb") ## creation en local du nouveau fichier + fp.write(data) ## ajout des donnees du fichier compresse dans le fichier local + fp.close() + zfile.close() + + return folderName ## Tested with python 2.6.6 -peakMotifsVersion = '0.1 - 30/01/2015' +peakMotifsVersion = '2.0 - 30/01/2015' ###########################################################' # server dictionary @@ -417,48 +464,15 @@ time.sleep(5) #logFile.write(str(nameFile)+"\n") - + #time.sleep(5) #while urllib.urlretrieve(urlResult, nameFile) #try: - ###########################################################' - ## Download RSAT results - urllib.urlretrieve(urlResult, nameFile) - #except IOError: - #logFile.write("\nResult URL is false") - #Logger.error("Result URL is false") - - #logFile.write("\n"+nameFile+"\n") - - ###########################################################' - ## Decompress results - #try: - zfile = zipfile.ZipFile(nameFile, 'r') - #except IOError: - #logFile.write("No zip file") - #Logger.error("No zip file") - - tempflag = 0 - folderName ="" - - for i in zfile.namelist(): ## On parcourt l'ensemble des fichiers de l'archive + folderName=recupRSATResult(urlResult,nameFile) - #logFile.write(i+"\n") - ############################### - if tempflag ==0: - folderName = i - - tempflag = 1 - ############################### - - if i.endswith('/'): ## S'il s'agit d'un repertoire, on se contente de creer le dossier - os.makedirs(i) - else: - data = zfile.read(i) ## lecture du fichier compresse - fp = open(i, "wb") ## creation en local du nouveau fichier - fp.write(data) ## ajout des donnees du fichier compresse dans le fichier local - fp.close() - zfile.close() + while(not(os.path.exists(folderName+"peak-motifs_synthesis.html"))): + os.popen("rm -rf "+folderName) + recupRSATResult(urlResult,nameFile) #logFile.write("\n"+folderName+"\n") #logFile.write("\n"+outGalaxyValue+"\n")