diff convertMatrix_wrapper.py @ 31:4f7cb568384f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convertMatrix_wrapper.py	Tue Sep 22 08:02:54 2015 -0400
@@ -0,0 +1,214 @@
+#! /usr/bin/python
+# -*- coding: utf8 -*-
+"""#Convert Matrix - 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 convert matrix results from RSAT server.
+#
+#
+#usage: convertMatrix_wrapper.py [-h] -matrix <MATRIX> -input_form <INPUT_FORM>
+#                                -output_form <OUTPUT_FORM>
+#                                [-return_type <RETURN_TYPE>] [-perm <PERM>]
+#                                [-rc <RC>] [-decimals <DECIMALS>] -server
+#                                <SERVEUR> -outGalaxy <OUT_GALAXY>
+#
+#optional arguments:
+#  -h, --help            show this help message and exit
+#  -matrix <MATRIX>, --matrix <MATRIX>
+#                        Matrix (or assembly or features) you want to convert.
+#  -input_form <INPUT_FORM>, --input_form <INPUT_FORM>
+#                        Input matrix format. Supported: alignace, assembly,
+#                        cb, clustal, consensus, feature, gibbs, infogibbs,
+#                        meme, motifsampler, tab, transfac.
+#  -output_form <OUTPUT_FORM>, --output_form <OUTPUT_FORM>
+#                        Output matrix format. Supported: consensus, patser,
+#                        tab, transfac.
+#  -return_type <RETURN_TYPE>, --return_type <RETURN_TYPE>
+#                        Result type (matrix content). Supported: consensus,
+#                        counts, frequencies, info, logo, margins, parameters,
+#                        profile, sites, wdistrib, weights.
+#  -perm <PERM>, --perm <PERM>
+#                        Number of permuted matrices to return.
+#  -rc <RC>, --rc <RC>   Convert the matrix to its reverse complement if value
+#                        = 1.
+#  -decimals <DECIMALS>, --decimals <DECIMALS>
+#                        Number of decimals to print for real matrices
+#                        (frequencies, weights, information) or to compute
+#                        score distributions.
+#  -server <SERVEUR>, --server <SERVEUR>
+#  -outGalaxy <OUT_GALAXY>, --outGalaxy <OUT_GALAXY>
+#
+###########################################################"""
+__author__ =  'Jocelyn Brayet'
+convertMatrixVersion = '0.1 - 06/03/2015'
+
+
+###########################################################'
+## 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.convert_matrix(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 = {
+    
+    #http://protists.rsat.eu/
+    "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 convert-matrix results from RSAT server.', epilog='Version '+convertMatrixVersion)
+
+
+    ########### convert matrix arguments ####################
+
+    parser.add_argument('-matrix', '--matrix', metavar='<MATRIX>', type=argparse.FileType('r'), nargs=1, help='Matrix (or assembly or features) you want to convert.', required=True)
+    parser.add_argument('-input_form', '--input_form', metavar='<INPUT_FORM>', type=str, nargs=1, help='Input matrix format. Supported: alignace, assembly, cb, clustal, consensus, feature, gibbs, infogibbs, meme, motifsampler, tab, transfac.', required=True)
+    parser.add_argument('-output_form', '--output_form', metavar='<OUTPUT_FORM>', type=str, nargs=1, help='Output matrix format. Supported: consensus, patser, tab, transfac.', required=True)
+    parser.add_argument('-return_type', '--return_type', metavar='<RETURN_TYPE>', type=str, nargs=1, help='Result type (matrix content). Supported: consensus, counts, frequencies, info, logo, margins, parameters, profile, sites, wdistrib, weights.', required=False)
+    parser.add_argument('-perm', '--perm', metavar='<PERM>', type=int, nargs=1, help='Number of permuted matrices to return.', 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_file = args.matrix[0].read()
+    serverValue = testNone(args.server)
+    outGalaxyValue = testNone(args.outGalaxy)
+    inputFormValue = testNone(args.input_form)
+    outputFormValue = testNone(args.output_form)
+    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)' % (
+        convertMatrixVersion, 
+        os.path.basename( __file__ ),
+        platform.python_version(), 
+        platform.system()
+    )
+    
+    httpHeaders = {'User-agent': userAgent}
+    client.set_options(headers=httpHeaders)
+    client.set_options(timeout=300)
+    
+    
+    convertMatrixRequest = {
+        
+        'matrix' : matrix_file,
+        'from' : inputFormValue,
+        'to' : outputFormValue,
+        'output' : 'both',
+        'return' : returnTypeValue,
+        'perm' : permValue,
+        'rc' : rcValue,
+        'decimals' : decimalsValue
+    
+        
+    }
+    
+      
+    result = call_run_service(rsat_service, convertMatrixRequest)
+    
+    print url
+    
+    print "###############################################"
+    print "Command performed on server"
+    print result.command
+    print "###############################################"
+    print "Result"
+    print result.server
+    
+    
+    nameFile = "convert-matrix_results.txt"
+    
+    urlResult=result.server.replace("$RSAT/public_html/",url.replace("web_services/RSATWS.wsdl",""))
+    
+    urllib.urlretrieve(urlResult, nameFile)
+    
+    os.popen("cp "+nameFile+" "+outGalaxyValue)
+
+