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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 """#oligo analysis 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 #Analysis of oligomer occurrences in nucleotidic of peptidic sequences.
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23 #
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24 ###########################################################'
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25 #
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26 # Client to have list RSAT oligo analysis.
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27 #
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28 #
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29 #usage: oligo-analysis_soap.py [-h] -sequence_file <SEQUENCE_FILE> -length
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30 # <LENGTH> -organism <ORGANISM> -server <SERVEUR>
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31 #
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32 #optional arguments:
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33 # -h, --help show this help message and exit
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34 # -sequence_file <SEQUENCE_FILE>, --sequence_file <SEQUENCE_FILE>
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35 # Input sequence (FASTA file).
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36 # -length <LENGTH>, --length <LENGTH>
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37 # Oligomer length.
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38 # -organism <ORGANISM>, --organism <ORGANISM>
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39 # Organism.
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40 # -stats <STATS>, --stats <STATS>
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41 # List of statistics to return. Supported:occ, mseq,
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42 # freq, proba, ratio, zscore, like, pos, rank.
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43 # -server <SERVEUR>, --server <SERVEUR>
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44 #
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45 #Version 0.1 - 16/04/2015
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46 #
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47 #
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48 ###########################################################'"""
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49 __author__ = 'Jocelyn Brayet'
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50 oligoAnalysisVersion = '0.1 - 16/04/2015'
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51
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52 ###########################################################'
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53 ## Import
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54
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55 import argparse
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56 import os
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57 import urllib
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58 from suds.client import Client
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59 import platform
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60
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61 ###########################################################'
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62
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63 ################################ functions ############################################################
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64 ## Define a function to make a service perform the desired request using provided arguments
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65 def call_run_service(rsat_service, args):
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66 """
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67 Run job in RSAT server.
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68 service -> RSAT web service
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69 args -> web service request
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70 """
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71
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72 result = rsat_service.oligo_analysis(args)
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73 return result
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74
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75 def testNone(argument):
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76 """
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77 Test if argument is None or not.
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78 argument -> argument give by user
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79 """
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80
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81 if not argument is None:
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82 variable = argument[0]
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83 else:
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84 variable = ""
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85 return variable
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86
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87
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88 ###########################################################'
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89 # server dictionary
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90 serverDict = {
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91
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92 "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
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93 "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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94 "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
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95 "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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96 "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
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97 "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
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98
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99 }
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100
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101 ###########################################################'
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102
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103 if __name__ == '__main__':
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104
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105 parser = argparse.ArgumentParser(description='Analysis of oligomer occurrences in nucleotidic of peptidic sequences.', epilog='Version '+oligoAnalysisVersion)
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106
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107 ########### compare matrices arguments ####################
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108
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109 parser.add_argument('-sequence_file', '--sequence_file', metavar='<SEQUENCE_FILE>', type=argparse.FileType('r'), nargs=1, help='Input sequence (FASTA file).', required=True)
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110 parser.add_argument('-length', '--length', metavar='<LENGTH>', type=int, nargs=1, help='Oligomer length.', required=True)
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111 parser.add_argument('-organism', '--organism', metavar='<ORGANISM>', type=str, nargs=1, help='Organism.', required=True)
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112 parser.add_argument('-stats', '--stats', metavar='<STATS>', type=str, nargs=1, help='List of statistics to return. Supported:occ, mseq, freq, proba, ratio, zscore, like, pos, rank.', required=False)
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113
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114 ########### galaxy arguments ##############################
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115 parser.add_argument('-server', '--server', metavar='<SERVEUR>', type=str, nargs=1, required=True)
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116 parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
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117 ###########################################################
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118
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119 args = parser.parse_args()
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120
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121 sequence_file = args.sequence_file[0].read()
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122 serverValue = testNone(args.server)
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123 length = testNone(args.length)
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124 organism = testNone(args.organism)
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125 stats = testNone(args.stats)
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126 outGalaxyValue = testNone(args.outGalaxy)
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127
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128 ###########################################################'
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129 ## Create the SOAP client to request the RSAT service
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130
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131
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132 # Load Client class from suds
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133 # Define URL for RSAT services
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134 url = serverDict[serverValue]
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135 # Create the client
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136 client = Client(url)
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137
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138 # Need service interface to perform requests
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139 rsat_service = client.service
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140
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141 #print client
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142
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143 # Define client header
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144 userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
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145 oligoAnalysisVersion,
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146 os.path.basename( __file__ ),
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147 platform.python_version(),
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148 platform.system()
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149 )
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150
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151 httpHeaders = {'User-agent': userAgent}
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152 client.set_options(headers=httpHeaders)
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153 client.set_options(timeout=300)
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154
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155
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156 oligoAnalysisRequest = {
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157
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158 'output' : 'both',
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159 'format' : 'fasta',
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160 'sequence' : sequence_file,
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161 'length' : length,
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162 'organism' : organism,
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163 'stats' : stats
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164
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165 }
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166
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167
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168 result = call_run_service(rsat_service, oligoAnalysisRequest)
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169
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170
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171 print url
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172
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173 print "###############################################"
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174 print "Command performed on server"
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175 print result.command
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176 print "###############################################"
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177 print "Result"
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178 print result.server
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179
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180 nameFile = "oligo-analysis_results.txt"
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181
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182 urlResult=result.server.replace("$RSAT/public_html/",url.replace("web_services/RSATWS.wsdl",""))
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183
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184 print urlResult
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185
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186 urllib.urlretrieve(urlResult, nameFile)
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187
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188 os.popen("cp "+nameFile+" "+outGalaxyValue)
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189
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190
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191
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