comparison compareMatrices_wrapper.py @ 29:b34046b02556 draft

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29:b34046b02556

#! /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)