diff compareMatrices_wrapper.py @ 29:b34046b02556 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compareMatrices_wrapper.py	Tue Sep 22 08:02:35 2015 -0400
@@ -0,0 +1,177 @@
+#! /usr/bin/python
+# -*- coding: utf8 -*-
+"""#Compare Matrices - developed by Jocelyn Brayet <[e-mail]>
+#Copyright (C) 2015  Institut Curie
+#
+#This program is free software: you can redistribute it and/or modify
+#it under the terms of the GNU General Public License as published by
+#the Free Software Foundation, either version 3 of the License, or
+#(at your option) any later version.
+#
+#This program is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#GNU General Public License for more details.
+#
+#You should have received a copy of the GNU General Public License
+#along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+###########################################################'
+# 
+#Client to download compare matrices results from RSAT server.
+#
+###########################################################'"""
+
+__author__ =  'Jocelyn Brayet'
+compareMatricesVersion = '0.1 - 14/04/2015'
+
+
+###########################################################'
+## Import
+
+import argparse
+import os
+import urllib
+from suds.client import Client
+import platform
+
+###########################################################'
+
+################################ functions ############################################################
+## Define a function to make a service perform the desired request using provided arguments
+def call_run_service(service, args):
+	"""
+	Run job in RSAT server.
+		service -> RSAT web service
+		args -> web service request 	 
+	"""
+	
+	result = rsat_service.compare_matrices(args)
+	return result
+
+def testNone(argument):
+	"""
+	Test if argument is None or not.
+		argument -> argument give by user
+	"""
+
+	if not argument is None:
+		variable = argument[0]
+	else:
+		variable = ""
+	return variable
+
+###########################################################'
+# server dictionary
+serverDict = {
+    
+    "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
+    "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
+    "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
+    "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
+    "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
+    "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
+    
+    }
+
+###########################################################'
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser(description='Client to download compare matrices results from RSAT server.', epilog='Version '+compareMatricesVersion)
+
+
+    ########### compare matrices arguments ####################
+
+    parser.add_argument('-matrix_1', '--matrix_1', metavar='<MATRIX_1>', type=argparse.FileType('r'), nargs=1, help='The first input containing one or several matrices.', required=True)
+    parser.add_argument('-matrix_2', '--matrix_2', metavar='<MATRIX_2>', type=argparse.FileType('r'), nargs=1, help='The second input containing one or several matrices.', required=True)
+    parser.add_argument('-format1', '--format1', metavar='<FORMAT_1>', type=str, nargs=1, help='Martix format for the first input. Supported fields: tab, cb, consensus, gibbs, meme, assembly.', required=True)
+    parser.add_argument('-format2', '--format2', metavar='<FORMAT_2>', type=str, nargs=1, help='Martix format for the second input. Supported fields: tab, cb, consensus, gibbs, meme, assembly.', required=True)
+    parser.add_argument('-returnResults', '--returnResults', metavar='<RETURN_RESULTS>', type=str, nargs=1, help='List of fields to return (only valid for the formats "profiles" and "matches").', required=False)
+    #parser.add_argument('-rc', '--rc', metavar='<RC>', type=int, nargs=1, help='Convert the matrix to its reverse complement if value = 1.', required=False)
+    #parser.add_argument('-decimals', '--decimals', metavar='<DECIMALS>', type=int, nargs=1, help='Number of decimals to print for real matrices (frequencies, weights, information) or to compute score distributions.', required=False)
+
+    ########### galaxy arguments ##############################
+    parser.add_argument('-server', '--server', metavar='<SERVEUR>', type=str, nargs=1, required=True)
+    parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
+    ###########################################################
+
+    args = parser.parse_args()
+
+    matrix_1 = args.matrix_1[0].read()
+    matrix_2 = args.matrix_2[0].read()
+    serverValue = testNone(args.server)
+    format1 = testNone(args.format1)
+    format2 = testNone(args.format2)
+    returnValue = testNone(args.returnResults)
+    outGalaxyValue = testNone(args.outGalaxy)
+    #returnTypeValue = testNone(args.return_type)
+    #permValue = testNone(args.perm)
+    #rcValue = testNone(args.rc)
+    #decimalsValue = testNone(args.decimals)
+    
+    ###########################################################'
+    ## Create the SOAP client to request the RSAT service
+    
+    
+    # Load Client class from suds
+    # Define URL for RSAT services 
+    url =  serverDict[serverValue]
+    # Create the client
+    client = Client(url)
+    
+    # Need service interface to perform requests
+    rsat_service = client.service
+    
+    #print client
+
+    # Define client header
+    userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
+        compareMatricesVersion, 
+        os.path.basename( __file__ ),
+        platform.python_version(), 
+        platform.system()
+    )
+    
+    httpHeaders = {'User-agent': userAgent}
+    client.set_options(headers=httpHeaders)
+    client.set_options(timeout=300)
+    
+
+    compareMatricesRequest = {
+        
+       	'output' : 'both',
+	'matrix_1' : matrix_1,
+	'matrix_2' : matrix_2,
+	'format1' : format1,
+	'format2' : format2,
+	'return' : returnValue
+   
+    }
+
+      
+    result = call_run_service(rsat_service, compareMatricesRequest)
+
+    
+    print url
+
+    print "###############################################"
+    print "Command performed on server"
+    print result.command
+    print "###############################################"
+    print "Result"
+    print result.server
+    
+    nameFile = "test_compare_matrices"
+    
+    urlResult=result.server.replace("$RSAT/public_html/",url.replace("web_services/RSATWS.wsdl",""))+"/.tab"
+    
+    urllib.urlretrieve(urlResult, nameFile)
+    
+    os.popen("cp "+nameFile+" "+outGalaxyValue)
+
+
+
+
+