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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 """#dyad 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 spaced dyads in a set of DNA sequences.
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23 #
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24 ###########################################################'
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25 #
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26 #usage: dyad-analysis_soap.py [-h] -sequence_file <SEQUENCE_FILE> -length
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27 # <LENGTH> -organism <ORGANISM> -spacing <SPACING>
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28 # [-stats <STATS>] [-type <TYPE>] -server <SERVEUR>
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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 # -sequence_file <SEQUENCE_FILE>, --sequence_file <SEQUENCE_FILE>
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33 # Input sequence (FASTA file).
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34 # -length <LENGTH>, --length <LENGTH>
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35 # Dyad length.
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36 # -organism <ORGANISM>, --organism <ORGANISM>
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37 # Organism.
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38 # -spacing <SPACING>, --spacing <SPACING>
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39 # Spacing between elements of the dyads.
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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 # -type <TYPE>, --type <TYPE>
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44 # Four types are accepted: dr (direct repeats: the
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45 # second element is the same as the first one); ir
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46 # (inverted repeats: the second element is the revers
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47 # complement of the first one); rep (repeats: direct and
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48 # inverted repeats are evaluated); any
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49 # -server <SERVEUR>, --server <SERVEUR>
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50 #
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51 #Version 0.1 - 16/04/2015
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52 #
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53 ###########################################################'"""
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54 __author__ = 'Jocelyn Brayet'
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55 dyadAnalysisVersion = '0.1 - 16/04/2015'
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56
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57 ###########################################################'
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58 ## Import
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59
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60 import argparse
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61 import os
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62 import urllib
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63 from suds.client import Client
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64 import platform
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65
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66 ###########################################################'
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67
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68 ################################ functions ############################################################
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69 ## Define a function to make a service perform the desired request using provided arguments
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70 def call_run_service(rsat_service, args):
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71 """
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72 Run job in RSAT server.
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73 service -> RSAT web service
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74 args -> web service request
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75 """
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76
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77 result = rsat_service.dyad_analysis(args)
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78 return result
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79
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80 def testNone(argument):
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81 """
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82 Test if argument is None or not.
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83 argument -> argument give by user
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84 """
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85
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86 if not argument is None:
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87 variable = argument[0]
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88 else:
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89 variable = ""
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90 return variable
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91
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92
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93 ###########################################################'
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94 # server dictionary
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95 serverDict = {
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96
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97 "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
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98 "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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99 "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
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100 "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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101 "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
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102 "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
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103
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104 }
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105
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106 ###########################################################'
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107
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108 if __name__ == '__main__':
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109
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110 parser = argparse.ArgumentParser(description='Analysis of spaced dyads in a set of DNA sequences.', epilog='Version '+dyadAnalysisVersion)
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111
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112 ########### compare matrices arguments ####################
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113
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114 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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115 parser.add_argument('-length', '--length', metavar='<LENGTH>', type=int, nargs=1, help='Dyad length.', required=True)
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116 parser.add_argument('-organism', '--organism', metavar='<ORGANISM>', type=str, nargs=1, help='Organism.', required=True)
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117 parser.add_argument('-spacing', '--spacing', metavar='<SPACING>', type=int, nargs=1, help='Spacing between elements of the dyads.', required=True)
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118 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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119 parser.add_argument('-type', '--type', metavar='<TYPE>', type=str, nargs=1, help='Four types are accepted: dr (direct repeats: the second element is the same as the first one); ir (inverted repeats: the second element is the revers complement of the first one); rep (repeats: direct and inverted repeats are evaluated); any', required=False)
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120
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121
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122
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123 ########### galaxy arguments ##############################
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124 parser.add_argument('-server', '--server', metavar='<SERVEUR>', type=str, nargs=1, required=True)
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125 parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
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126 ###########################################################
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127
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128 args = parser.parse_args()
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129
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130 sequence_file = args.sequence_file[0].read()
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131 serverValue = testNone(args.server)
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132 length = testNone(args.length)
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133 organism = testNone(args.organism)
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134 spacing = testNone(args.spacing)
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135 stats = testNone(args.stats)
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136 typeValue = testNone(args.type)
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137 outGalaxyValue = testNone(args.outGalaxy)
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138
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139
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140 ###########################################################'
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141 ## Create the SOAP client to request the RSAT service
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142
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143
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144 # Load Client class from suds
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145 # Define URL for RSAT services
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146 url = serverDict[serverValue]
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147 # Create the client
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148 client = Client(url)
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149
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150 # Need service interface to perform requests
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151 rsat_service = client.service
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152
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153 #print client
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154
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155 # Define client header
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156 userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
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157 dyadAnalysisVersion,
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158 os.path.basename( __file__ ),
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159 platform.python_version(),
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160 platform.system()
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161 )
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162
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163 httpHeaders = {'User-agent': userAgent}
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164 client.set_options(headers=httpHeaders)
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165 client.set_options(timeout=300)
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166
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167
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168 dyadAnalysisRequest = {
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169
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170 'output' : 'both',
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171 'format' : 'fasta',
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172 'sequence' : sequence_file,
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173 'length' : length,
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174 'organism' : organism,
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175 'spacing' : spacing,
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176 'stats' : stats,
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177 'type' : typeValue
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178
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179 }
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180
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181
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182 result = call_run_service(rsat_service, dyadAnalysisRequest)
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183
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184
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185 print url
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186
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187 print "###############################################"
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188 print "Command performed on server"
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189 print result.command
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190 print "###############################################"
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191 print "Result"
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192 print result.server
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193
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194 nameFile = "dyad_analysis_results.txt"
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195
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196 urlResult=result.server.replace("$RSAT/public_html/",url.replace("web_services/RSATWS.wsdl",""))
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197
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198 print urlResult
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199
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200 urllib.urlretrieve(urlResult, nameFile)
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201
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202
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203 os.popen("cp "+nameFile+" "+outGalaxyValue)
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204
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205
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206
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207
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