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1 #! /usr/bin/python
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2 # -*- coding: utf8 -*-
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3 """#Convert Matrix - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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4 #Copyright (C) 2015 Institut Curie
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5 #
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6 #This program is free software: you can redistribute it and/or modify
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7 #it under the terms of the GNU General Public License as published by
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8 #the Free Software Foundation, either version 3 of the License, or
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9 #(at your option) any later version.
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10 #
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11 #This program is distributed in the hope that it will be useful,
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12 #but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 #MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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14 #GNU General Public License for more details.
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15 #
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16 #You should have received a copy of the GNU General Public License
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17 #along with this program. If not, see <http://www.gnu.org/licenses/>.
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18 #
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19 ###########################################################'
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20 #
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21 #Client to download convert matrix results from RSAT server.
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22 #
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23 #
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24 #usage: convertMatrix_wrapper.py [-h] -matrix <MATRIX> -input_form <INPUT_FORM>
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25 # -output_form <OUTPUT_FORM>
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26 # [-return_type <RETURN_TYPE>] [-perm <PERM>]
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27 # [-rc <RC>] [-decimals <DECIMALS>] -server
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28 # <SERVEUR> -outGalaxy <OUT_GALAXY>
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29 #
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30 #optional arguments:
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31 # -h, --help show this help message and exit
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32 # -matrix <MATRIX>, --matrix <MATRIX>
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33 # Matrix (or assembly or features) you want to convert.
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34 # -input_form <INPUT_FORM>, --input_form <INPUT_FORM>
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35 # Input matrix format. Supported: alignace, assembly,
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36 # cb, clustal, consensus, feature, gibbs, infogibbs,
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37 # meme, motifsampler, tab, transfac.
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38 # -output_form <OUTPUT_FORM>, --output_form <OUTPUT_FORM>
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39 # Output matrix format. Supported: consensus, patser,
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40 # tab, transfac.
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41 # -return_type <RETURN_TYPE>, --return_type <RETURN_TYPE>
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42 # Result type (matrix content). Supported: consensus,
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43 # counts, frequencies, info, logo, margins, parameters,
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44 # profile, sites, wdistrib, weights.
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45 # -perm <PERM>, --perm <PERM>
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46 # Number of permuted matrices to return.
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47 # -rc <RC>, --rc <RC> Convert the matrix to its reverse complement if value
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48 # = 1.
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49 # -decimals <DECIMALS>, --decimals <DECIMALS>
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50 # Number of decimals to print for real matrices
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51 # (frequencies, weights, information) or to compute
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52 # score distributions.
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53 # -server <SERVEUR>, --server <SERVEUR>
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54 # -outGalaxy <OUT_GALAXY>, --outGalaxy <OUT_GALAXY>
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55 #
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56 ###########################################################"""
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57 __author__ = 'Jocelyn Brayet'
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58 convertMatrixVersion = '0.1 - 06/03/2015'
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59
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60
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61 ###########################################################'
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62 ## Import
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63
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64 import argparse
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65 import os
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66 import urllib
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67 from suds.client import Client
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68 import platform
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69
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70 ###########################################################'
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71
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72 ################################ functions ############################################################
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73 ## Define a function to make a service perform the desired request using provided arguments
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74 def call_run_service(service, args):
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75 """
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76 Run job in RSAT server.
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77 service -> RSAT web service
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78 args -> web service request
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79 """
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80
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81 result = rsat_service.convert_matrix(args)
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82 return result
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83
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84 def testNone(argument):
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85 """
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86 Test if argument is None or not.
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87 argument -> argument give by user
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88 """
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89
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90 if not argument is None:
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91 variable = argument[0]
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92 else:
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93 variable = ""
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94 return variable
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95
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96 ###########################################################'
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97
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98 ###########################################################'
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99 # server dictionary
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100 serverDict = {
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101
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102 #http://protists.rsat.eu/
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103 "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
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104 "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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105 "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
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106 "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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107 "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
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108 "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
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109
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110 }
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111
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112 ###########################################################'
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113
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114 if __name__ == '__main__':
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115
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116 parser = argparse.ArgumentParser(description='Client to download convert-matrix results from RSAT server.', epilog='Version '+convertMatrixVersion)
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117
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118
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119 ########### convert matrix arguments ####################
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120
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121 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)
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122 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)
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123 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)
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124 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)
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125 parser.add_argument('-perm', '--perm', metavar='<PERM>', type=int, nargs=1, help='Number of permuted matrices to return.', required=False)
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126 parser.add_argument('-rc', '--rc', metavar='<RC>', type=int, nargs=1, help='Convert the matrix to its reverse complement if value = 1.', required=False)
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127 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)
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128
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129
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130
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131 ########### galaxy arguments ##############################
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132 parser.add_argument('-server', '--server', metavar='<SERVEUR>', type=str, nargs=1, required=True)
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133 parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
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134 ###########################################################
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135
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136 args = parser.parse_args()
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137
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138
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139 matrix_file = args.matrix[0].read()
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140 serverValue = testNone(args.server)
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141 outGalaxyValue = testNone(args.outGalaxy)
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142 inputFormValue = testNone(args.input_form)
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143 outputFormValue = testNone(args.output_form)
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144 returnTypeValue = testNone(args.return_type)
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145 permValue = testNone(args.perm)
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146 rcValue = testNone(args.rc)
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147 decimalsValue = testNone(args.decimals)
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148
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149 ###########################################################'
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150 ## Create the SOAP client to request the RSAT service
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151
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152
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153 # Load Client class from suds
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154 # Define URL for RSAT services
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155 url = serverDict[serverValue]
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156 # Create the client
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157 client = Client(url)
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158
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159 # Need service interface to perform requests
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160 rsat_service = client.service
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161
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162
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163 #print client
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164
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165
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166 # Define client header
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167 userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
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168 convertMatrixVersion,
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169 os.path.basename( __file__ ),
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170 platform.python_version(),
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171 platform.system()
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172 )
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173
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174 httpHeaders = {'User-agent': userAgent}
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175 client.set_options(headers=httpHeaders)
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176 client.set_options(timeout=300)
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177
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178
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179 convertMatrixRequest = {
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180
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181 'matrix' : matrix_file,
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182 'from' : inputFormValue,
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183 'to' : outputFormValue,
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184 'output' : 'both',
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185 'return' : returnTypeValue,
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186 'perm' : permValue,
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187 'rc' : rcValue,
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188 'decimals' : decimalsValue
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189
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190
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191 }
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192
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193
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194 result = call_run_service(rsat_service, convertMatrixRequest)
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195
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196 print url
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197
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198 print "###############################################"
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199 print "Command performed on server"
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200 print result.command
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201 print "###############################################"
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202 print "Result"
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203 print result.server
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204
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205
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206 nameFile = "convert-matrix_results.txt"
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207
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208 urlResult=result.server.replace("$RSAT/public_html/",url.replace("web_services/RSATWS.wsdl",""))
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209
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210 urllib.urlretrieve(urlResult, nameFile)
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211
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212 os.popen("cp "+nameFile+" "+outGalaxyValue)
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213
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214
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