Mercurial > repos > jbrayet > rsat

changeset 52:a1d369ead6d7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jbrayet
date Tue, 29 Sep 2015 08:25:39 -0400
parents 9e193aa2b9d2
children
files peakMotifs_wrapper.py
diffstat 1 files changed, 7 insertions(+), 108 deletions(-) [+]
line wrap: on
line diff
--- a/peakMotifs_wrapper.py	Tue Sep 29 07:39:19 2015 -0400
+++ b/peakMotifs_wrapper.py	Tue Sep 29 08:25:39 2015 -0400
@@ -112,65 +112,6 @@
 import platform
 from suds.client import Client
 
-###########################################################'
-
-###########################################################'
-## Define log options for suds
-
-# Import log package
-#import logging
-
-# Import log package
-#import logging
-# création de l'objet logger qui va nous servir à écrire dans les logs
-#logger = logging.getLogger()
-# on met le niveau du logger à DEBUG, comme ça il écrit tout
-#logger.setLevel(logging.DEBUG)
-# Configure log of suds clients to DEBUG for verbose output concerning Client request
-#logging.getLogger('suds.client').setLevel(logging.ERROR)
-#logging.getLogger('suds.transport').setLevel(logging.ERROR)
-#logging.getLogger('suds.xsd.schema').setLevel(logging.ERROR)
-#logging.getLogger('suds.wsdl').setLevel(logging.ERROR)
-
-
-# création d'un second handler qui va rediriger chaque écriture de log
-# sur la console
-#steam_handler = logging.StreamHandler()
-#steam_handler.setLevel(logging.DEBUG)
-#logger.addHandler(steam_handler)
-
-#logger.info('Hello')
-
-#print(client.factory.create('peak_motifs'))
-
-#	  (PeakMotifsRequest){
-#		 output = None -> ok
-#		 verbosity = None
-#		 test = None -> ok
-#		 tmp_test_infile = None
-#		 control = None
-#		 tmp_control_infile = None
-#		 max_seq_length = None
-#		 max_motif_number = None
-#		 ref_motif = None
-#		 top_peaks = None
-#		 min_length = None
-#		 max_length = None
-#		 markov = None
-#		 min_markov = None
-#		 max_markov = None
-#		 noov = None
-#		 class_int = None
-#		 str = None
-#		 graph_title = None
-#		 image_format = None
-#		 disco = None
-#		 source = None
-#		 task = None
-#	  }
-# }
-
-
 ################################ functions ############################################################
 ## Define a function to make a service perform the desired request using provided arguments
 def call_run_service(service, args):
@@ -222,18 +163,10 @@
 	###########################################################'
 	## 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 =""
@@ -417,16 +350,6 @@
 	## Run job in RSAT server
 	result = call_run_service(rsat_service, peakMotifsRequest)
 
-	#logFile = open("/bioinfo/users/jbrayet/Bureau/peak_motifs.log","w")
-
-	#logFile.write("###############################################\n")
-	#logFile.write("Command performed on server\n")
-	#logFile.write(result.command)
-	#logFile.write("\n")
-	#logFile.write("###############################################\n")
-	#logFile.write("Result\n")
-	#logFile.write(result.server)
-
 	print("###############################################\n")
 	print("Command performed on server\n")
 	print(result.command)
@@ -451,60 +374,36 @@
 		}
 	"""
 
-	nameFile = "peak-motifs_results.zip"
+	nameFile = "peak-motifs_archive.zip"
 	urlResult=buildZipUrl(result.server)
 	print urlResult
 
-	#ogFile.write("\n"+urlResult)
-
 	###########################################################'
 	## Wait RSAT server
 	while urllib.urlopen(urlResult).getcode() != 200:
-	#logFile.write(str(urllib.urlopen(urlResult).getcode())+"\n")
 		time.sleep(5)
 
-	#logFile.write(str(nameFile)+"\n")
-	#time.sleep(5)
-	#while urllib.urlretrieve(urlResult, nameFile) 
-	#try:
-
 	folderName=recupRSATResult(urlResult,nameFile)
 	
 	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")
-
         os.popen("cp "+folderName+"peak-motifs_synthesis.html "+outGalaxyValue)
-	os.popen("cp "+nameFile+" "+folderName)
-        #logFile.close()
-        #os.popen("sed -i \"1iHHEELLLOOO\" "+outGalaxyValue)
-        #os.popen("sed -i \"1i<style type=\'text/css\'></style>\" "+outGalaxyValue)
 
         ###########################################################'
         ##Create results folder name
-        outGalaxyValueDir = outGalaxyValue.replace(".dat","_files")
-
-        #logFile.write("\noutGalaxyValueDir : " +outGalaxyValueDir)
-
-        #logFile.close()
 
         # Create results folder
-        os.popen("mkdir "+outGalaxyValueDir)
+	outGalaxyValueDir = outGalaxyValue.replace(".dat","_files")
+	os.popen("mkdir "+outGalaxyValueDir)
 
         # Copy results files in results folder
-        os.popen("cp -R "+folderName+"data " + outGalaxyValueDir+"/data")
-        os.popen("cp -R "+folderName+"reports " + outGalaxyValueDir+"/reports")
-        os.popen("cp -R "+folderName+"results " + outGalaxyValueDir+"/results")
+
+	os.popen("cp "+nameFile+" "+outGalaxyValueDir+"/"+nameFile)
+        os.popen("cp -R "+folderName+"* " + outGalaxyValueDir+"/")
         
         if not outGalaxyValue2 =="":
             os.popen("cp "+folderName+"results/sites/peak-motifs_all_motifs_seqcoord.bed "+outGalaxyValue2)
         
-        
-        
-
-
-
-
+