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1 #! /usr/bin/python
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2 # -*- coding: utf8 -*-
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3
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4 """#supported motif databases soap - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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5 #Copyright (C) 2015 Institut Curie
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6 #
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7 #This program is free software: you can redistribute it and/or modify
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8 #it under the terms of the GNU General Public License as published by
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9 #the Free Software Foundation, either version 3 of the License, or
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10 #(at your option) any later version.
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11 #
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12 #This program is distributed in the hope that it will be useful,
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13 #but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 #MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 #GNU General Public License for more details.
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16 #
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17 #You should have received a copy of the GNU General Public License
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18 #along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 #
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20 ###########################################################'
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21 #
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22 #Recup motif databases to each RSAT server and create loc files for Galaxy.
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23 #
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24 ###########################################################'
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25 #
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26 # List RSAT suppported motif databases.
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27 #
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28 #
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29 #usage: supported-motif-databases_soap.py [-h] -galaxyPath <GALAXY_PATH>
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30 #
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31 #optional arguments:
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32 # -h, --help show this help message and exit
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33 # -galaxyPath <GALAXY_PATH>, --galaxyPath <GALAXY_PATH>
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34 # Galaxy tool_data_path directory (e.i. /myGalaxy
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35 # /galaxy-dist/tool-data)
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36 #
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37 #Version 0.1 - 27/05/2015
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38 #
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39 ###########################################################'"""
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40 __author__ = 'Jocelyn Brayet'
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41 supportedMotifDatabasesVersion = '0.1 - 27/05/2015'
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42
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43 ###########################################################'
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44 ## Import
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45
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46 import argparse
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47 import os
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48 import urllib
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49 from suds.client import Client
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50 import platform
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51
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52 ###########################################################'
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53
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54 ################################ functions ############################################################
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55 ## Define a function to make a service perform the desired request using provided arguments
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56 def call_run_service(rsat_service, args):
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57 """
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58 Run job in RSAT server.
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59 service -> RSAT web service
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60 args -> web service request
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61 """
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62
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63 result = rsat_service.supported_motif_databases(args)
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64 return result
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65
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66 def testNone(argument):
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67 """
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68 Test if argument is None or not.
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69 argument -> argument give by user
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70 """
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71
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72 if not argument is None:
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73 variable = argument[0]
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74 else:
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75 variable = ""
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76 return variable
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77
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78 def recupMotifDatabases(srv,request,dicServ):
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79
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80 """
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81 Recup RSAT organisms in each RSAT server.
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82 srv -> server key in server dictionary
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83 request -> job request
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84 dicServ -> server dictionary
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85 """
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86
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87 # Create the client
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88 client = Client(serverDict[srv])
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89 # Need service interface to perform requests
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90 rsat_service = client.service
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91
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92 print client
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93 # Define client header
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94
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95 userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
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96 supportedMotifDatabasesVersion,
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97 os.path.basename( __file__ ),
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98 platform.python_version(),
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99 platform.system()
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100 )
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101
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102 httpHeaders = {'User-agent': userAgent}
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103 client.set_options(headers=httpHeaders)
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104 client.set_options(timeout=300)
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105
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106 result = call_run_service(rsat_service, request)
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107
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108 ###########################################################'
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109 ## Display request results
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110
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111 print '###############################################'
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112 print 'Command performed on server'
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113 print ''
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114 print result.command
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115 print ''
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116 print '###############################################'
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117 print 'Result'
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118 print ''
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119 print result.client
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120
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121 return(result.client)
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122
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123 ###########################################################'
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124
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125 ###########################################################'
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126 # server dictionary
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127 serverDict = {
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128
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129 #http://protists.rsat.eu/
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130 "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
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131 "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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132 "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
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133 "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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134 "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
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135 "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
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136
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137 }
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138
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139
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140 if __name__ == '__main__':
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141
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142 # Create the parser
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143 parser = argparse.ArgumentParser(description='List RSAT suppported motif databases.', epilog='Version '+supportedMotifDatabasesVersion)
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144
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145 # List desired arguments
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146 #parser.add_argument('-r', '--return_param', metavar='<RETURN_PARAM>', type=str, nargs=1, help='Return fields. Supported: name,format,file,descr,version,url.', required=True)
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147 parser.add_argument('-galaxyPath', '--galaxyPath', metavar='<GALAXY_PATH>', type=str, nargs=1, help='Galaxy tool_data_path directory (e.i. /myGalaxy/galaxy-dist/tool-data)', required=True)
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148
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149 # Parse command line
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150 args = parser.parse_args()
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151
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152 # Get values to be used
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153 #output_return = testNone(args.return_param)
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154 galaxyPath = testNone(args.galaxyPath)
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155
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156 for srv in serverDict:
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157
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158 functionResult=""
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159 reslutsTab=list()
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160 finalTab=list()
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161
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162 supportedMotifDatabasesRequest = {
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163
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164 'output' : 'client',
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165 'return' : 'name'
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166
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167 }
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168
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169 functionResult=recupMotifDatabases(srv,supportedMotifDatabasesRequest,serverDict)
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170 reslutsTab=str(functionResult).split("\n")
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171 del reslutsTab[-1]
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172 resultsFile = open(galaxyPath+"/"+"RSAT_motif_databases_"+srv+".loc","w")
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173 for value in reslutsTab:
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174 if not value.startswith("#"):
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175 resultsFile.write(value+"\n")
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176 resultsFile.close()
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