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1 #! /usr/bin/python
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2 # -*- coding: utf8 -*-
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3 """#Peak Motifs - 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 peak-motifs results from RSAT server.
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22 #
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23 #
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24 #usage: peak-motifs_soap.py [-h] -test <TEST_FILE> [-control <CONTROL_FILE>]
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25 # [-max_seq_length <MAX_SEQ_LENGTH>]
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26 # [-max_motif_number <MAX_MOTIF_NUMBER>]
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27 # [-top_peaks <TOP_PEAKS>] [-min_length <MIN_LENGTH>]
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28 # [-max_length <MAX_LENGTH>] [-markov <MARKOV_MODEL>]
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29 # [-min_markov <MIN_MARKOV>]
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30 # [-max_markov <MAX_MARKOV>] [-noov <NOOV_DETECTION>]
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31 # [-class_int <CLASS_INT>] [-str <STR_SUMMED>]
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32 # [-graph_title <GRAPH_TITLE>]
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33 # [-image_format <IMAGE_FORMAT>]
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34 # [-disco [<DISCO_ALGORITHM> [<DISCO_ALGORITHM> ...]]]
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35 # [-source <SOURCE_FILE>] [-verb <VERBOSITY>]
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36 # [-ref_motif <REF_MOTIF>] -server <SERVEUR>
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37 #
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38 #optional arguments:
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39 # -h, --help show this help message and exit
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40 # -test <TEST_FILE>, --test_file <TEST_FILE>
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41 # Input test peak sequence in fasta format.
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42 # -control <CONTROL_FILE>, --control_file <CONTROL_FILE>
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43 # Input control peak sequence in fasta format.
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44 # -max_seq_length <MAX_SEQ_LENGTH>, --maxSeqLength <MAX_SEQ_LENGTH>
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45 # Maximal sequence length.
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46 # -max_motif_number <MAX_MOTIF_NUMBER>, --maxMotifNumber <MAX_MOTIF_NUMBER>
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47 # Maximal number of motifs (matrices) to return for
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48 # pattern discovery algorithms.
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49 # -top_peaks <TOP_PEAKS>, --topPeaks <TOP_PEAKS>
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50 # Restrict the analysis to the N peaks at the top of the
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51 # input sequence file.
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52 # -min_length <MIN_LENGTH>, --minLength <MIN_LENGTH>
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53 # Minimal oligonucleotide length.
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54 # -max_length <MAX_LENGTH>, --maxLength <MAX_LENGTH>
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55 # Maximal oligonucleotide length.
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56 # -markov <MARKOV_MODEL>, --markovModel <MARKOV_MODEL>
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57 # Order of the Markov model used to estimatd expected
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58 # oligonucleotide frequencies for oligo-analysis and
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59 # local-word-analysis.
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60 # -min_markov <MIN_MARKOV>, --minMarkov <MIN_MARKOV>
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61 # Minimal value for markov order. Use in combination
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62 # with the next option (max_markov).
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63 # -max_markov <MAX_MARKOV>, --maxMarkov <MAX_MARKOV>
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64 # Maximal value for markov order. Use in combination
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65 # with the previous option (min_markov).
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66 # -noov <NOOV_DETECTION>, --noovDetection <NOOV_DETECTION>
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67 # No overlapping of oligos allowed if value = 1.
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68 # -class_int <CLASS_INT>, --classInt <CLASS_INT>
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69 # Class interval for position-analysis. The width of the
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70 # position classes, in number of bases (default: 20).
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71 # -str <STR_SUMMED>, --strSummed <STR_SUMMED>
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72 # Oligonucleotide occurrences found on both stands are
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73 # summed (2) or not (1). Default is 2.
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74 # -graph_title <GRAPH_TITLE>, --graphTitle <GRAPH_TITLE>
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75 # Title displayed on top of the graphs.
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76 # -image_format <IMAGE_FORMAT>, --imageFormat <IMAGE_FORMAT>
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77 # Image format. All the formats supported by XYgraph can
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78 # be used.
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79 # -disco [<DISCO_ALGORITHM> [<DISCO_ALGORITHM> ...]], --discoAlgorithm [<DISCO_ALGORITHM> [<DISCO_ALGORITHM> ...]]
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80 # Specify the software tool(s) that will be used for
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81 # motif discovery
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82 # (oligos|dyads|positions|local_words|merged_words).
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83 # Several algorithms can be specified either by using a
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84 # comma-separated list of algorithms: -disco
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85 # oligos,dyads
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86 # -source <SOURCE_FILE>, --sourceFile <SOURCE_FILE>
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87 # Enter the source of the fasta sequence file. Supported
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88 # source: galaxy
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89 # -verb <VERBOSITY>, --verbosity <VERBOSITY>
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90 # Verbosity.
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91 # -ref_motif <REF_MOTIF>, --ref_motif <REF_MOTIF>
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92 # Motif annotated in some transcription factor database
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93 # (e.g. RegulonDB, Jaspar, TRANSFAC) for the
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94 # transcription factor of interest.
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95 # -server <SERVEUR>, --server <SERVEUR>
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96 # RSAT server
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97 # -outGalaxy <OUT_GALAXY>, --outGalaxy <OUT_GALAXY>
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98 #
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51
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99 #Version 2.0 - 30/01/2015 - Adapted from Jocelyn Brayet, France Genomique team
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100 #
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101 ###########################################################"""
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102 __author__ = 'Jocelyn Brayet'
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103
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104 ###########################################################'
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105 ## Import
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106
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107 import argparse
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108 import os
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109 import urllib
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110 import zipfile
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111 import time
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112 import platform
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113 from suds.client import Client
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114
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115 ###########################################################'
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116
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117 ###########################################################'
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118 ## Define log options for suds
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119
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120 # Import log package
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121 #import logging
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122
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123 # Import log package
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124 #import logging
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125 # création de l'objet logger qui va nous servir à écrire dans les logs
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126 #logger = logging.getLogger()
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127 # on met le niveau du logger à DEBUG, comme ça il écrit tout
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128 #logger.setLevel(logging.DEBUG)
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129 # Configure log of suds clients to DEBUG for verbose output concerning Client request
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130 #logging.getLogger('suds.client').setLevel(logging.ERROR)
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131 #logging.getLogger('suds.transport').setLevel(logging.ERROR)
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132 #logging.getLogger('suds.xsd.schema').setLevel(logging.ERROR)
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133 #logging.getLogger('suds.wsdl').setLevel(logging.ERROR)
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134
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135
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136 # création d'un second handler qui va rediriger chaque écriture de log
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137 # sur la console
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138 #steam_handler = logging.StreamHandler()
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139 #steam_handler.setLevel(logging.DEBUG)
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140 #logger.addHandler(steam_handler)
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141
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142 #logger.info('Hello')
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143
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144 #print(client.factory.create('peak_motifs'))
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145
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146 # (PeakMotifsRequest){
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147 # output = None -> ok
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148 # verbosity = None
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149 # test = None -> ok
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150 # tmp_test_infile = None
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151 # control = None
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152 # tmp_control_infile = None
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153 # max_seq_length = None
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154 # max_motif_number = None
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155 # ref_motif = None
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156 # top_peaks = None
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157 # min_length = None
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158 # max_length = None
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159 # markov = None
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160 # min_markov = None
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161 # max_markov = None
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162 # noov = None
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163 # class_int = None
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164 # str = None
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165 # graph_title = None
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166 # image_format = None
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167 # disco = None
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168 # source = None
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169 # task = None
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170 # }
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171 # }
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172
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173
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174 ################################ functions ############################################################
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175 ## Define a function to make a service perform the desired request using provided arguments
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176 def call_run_service(service, args):
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177 """
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178 Run job in RSAT server.
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179 service -> RSAT web service
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180 args -> web service request
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181 """
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182
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183 result = rsat_service.peak_motifs(args)
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184 return result
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185
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186 def testNone(argument):
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187 """
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188 Test if argument is None or not.
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189 argument -> argument give by user
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190 """
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191
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192 if not argument is None:
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193 variable = argument[0]
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194 else:
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195 variable = ""
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196 return variable
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197
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198
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199 ###########################################################'
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50
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200 ## Functions to recup results
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2
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201
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202 def buildZipUrl(algoResults):
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203 """
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204 Recup results give by RSAT server.
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50
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205 algoResults -> response gave by RSAT server
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2
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206 """
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207
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208 recupResult = str(algoResults)
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209 tabResults=recupResult.split("\n")
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210 urlZip = tabResults[4].replace("\t","")
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211
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212 return urlZip
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213
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50
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214 def recupRSATResult(urlResult,nameFile):
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215
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216 """
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217 Recup results give by RSAT server.
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218 urlResult -> URL gave by RSAT server
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219 nameFile -> name of zip file in Galaxy path
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220 """
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221
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222 ###########################################################'
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223 ## Download RSAT results
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224 urllib.urlretrieve(urlResult, nameFile)
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225 #except IOError:
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226 #logFile.write("\nResult URL is false")
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227 #Logger.error("Result URL is false")
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228 #logFile.write("\n"+nameFile+"\n")
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229
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230 ###########################################################'
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231 ## Decompress results
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232 #try:
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233 zfile = zipfile.ZipFile(nameFile, 'r')
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234 #except IOError:
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235 #logFile.write("No zip file")
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236 #Logger.error("No zip file")
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237
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238 tempflag = 0
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239 folderName =""
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240
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241 for i in zfile.namelist(): ## On parcourt l'ensemble des fichiers de l'archive
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242
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243 #logFile.write(i+"\n")
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244 ###############################
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245 if tempflag ==0:
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246 folderName = i
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247
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248 tempflag = 1
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249 ###############################
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250
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251 if i.endswith('/'): ## S'il s'agit d'un repertoire, on se contente de creer le dossier
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252 os.makedirs(i)
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253 else:
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254 data = zfile.read(i) ## lecture du fichier compresse
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255 fp = open(i, "wb") ## creation en local du nouveau fichier
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256 fp.write(data) ## ajout des donnees du fichier compresse dans le fichier local
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257 fp.close()
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258 zfile.close()
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259
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260 return folderName
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261
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262 ## Tested with python 2.6.6
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263 peakMotifsVersion = '2.0 - 30/01/2015'
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264
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265 ###########################################################'
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266 # server dictionary
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267 serverDict = {
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268
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269 "fr_ens":"http://rsat01.biologie.ens.fr/rsat/web_services/RSATWS.wsdl",
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270 "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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271 "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
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272 "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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273 "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
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274 "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
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275
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276 }
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277
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278 """
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279 serverDict = {
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280
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281 "fr_ens":"http://protists.rsat.eu/rsat/web_services/RSATWS.wsdl",
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282 "fr_mrs":"http://fungi.rsat.eu/rsat/web_services/RSATWS.wsdl",
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283 "fr_ro":"http://metazoa.rsat.eu/web_services/RSATWS.wsdl",
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284 "fr_mrs_2":"http://teaching.rsat.eu/rsat/web_services/RSATWS.wsdl",
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285 "es":"http://plants.rsat.eu/rsat/web_services/RSATWS.wsdl",
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286 "mx":"http://prokaryotes.rsat.eu/rsa-tools/web_services/RSATWS.wsdl"
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287
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288 }
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289 """
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290
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291 if __name__ == '__main__':
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292
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293 ########### peak motifs arguments ####################
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294 parser = argparse.ArgumentParser(description='Client to download peak-motifs results from RSAT server.', epilog='Version '+peakMotifsVersion)
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295
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296 parser.add_argument('-test', '--test_file', metavar='<TEST_FILE>', type=argparse.FileType('r'), nargs=1, help='Input test peak sequence in fasta format.', required=True)
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297 parser.add_argument('-control', '--control_file', metavar='<CONTROL_FILE>', type=argparse.FileType('r'), nargs=1, help='Input control peak sequence in fasta format.', required=False)
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298 parser.add_argument('-max_seq_length', '--maxSeqLength', metavar='<MAX_SEQ_LENGTH>', type=int, nargs=1, help='Maximal sequence length.', required=False)
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299 parser.add_argument('-max_motif_number', '--maxMotifNumber', metavar='<MAX_MOTIF_NUMBER>', type=int, nargs=1, help='Maximal number of motifs (matrices) to return for pattern discovery algorithms.', required=False)
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300 parser.add_argument('-top_peaks', '--topPeaks', metavar='<TOP_PEAKS>', type=int, nargs=1, help='Restrict the analysis to the N peaks at the top of the input sequence file.', required=False)
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301 parser.add_argument('-min_length', '--minLength', metavar='<MIN_LENGTH>', type=int, nargs=1, help='Minimal oligonucleotide length.', required=False)
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302 parser.add_argument('-max_length', '--maxLength', metavar='<MAX_LENGTH>', type=int, nargs=1, help='Maximal oligonucleotide length.', required=False)
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303 parser.add_argument('-markov', '--markovModel', metavar='<MARKOV_MODEL>', type=int, nargs=1, help='Order of the Markov model used to estimatd expected oligonucleotide frequencies for oligo-analysis and local-word-analysis.', required=False)
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304 parser.add_argument('-min_markov', '--minMarkov', metavar='<MIN_MARKOV>', type=int, nargs=1, help='Minimal value for markov order. Use in combination with the next option (max_markov).', required=False)
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305 parser.add_argument('-max_markov', '--maxMarkov', metavar='<MAX_MARKOV>', type=int, nargs=1, help='Maximal value for markov order. Use in combination with the previous option (min_markov).', required=False)
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306 parser.add_argument('-noov', '--noovDetection', metavar='<NOOV_DETECTION>', type=int, nargs=1, help='No overlapping of oligos allowed if value = 1.', required=False)
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307 parser.add_argument('-class_int', '--classInt', metavar='<CLASS_INT>', type=int, nargs=1, help='Class interval for position-analysis. The width of the position classes, in number of bases (default: 20).', required=False)
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308 parser.add_argument('-str', '--strSummed', metavar='<STR_SUMMED>', type=int, nargs=1, help='Oligonucleotide occurrences found on both stands are summed (2) or not (1). Default is 2.', required=False)
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309 parser.add_argument('-graph_title', '--graphTitle', metavar='<GRAPH_TITLE>', type=str, nargs=1, help='Title displayed on top of the graphs.', required=False)
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310 parser.add_argument('-image_format', '--imageFormat', metavar='<IMAGE_FORMAT>', type=str, nargs=1, help='Image format. All the formats supported by XYgraph can be used.', required=False)
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311 parser.add_argument('-disco', '--discoAlgorithm', metavar='<DISCO_ALGORITHM>', type=str, nargs='*', help='Specify the software tool(s) that will be used for motif discovery (oligos|dyads|positions|local_words|merged_words). Several algorithms can be specified either by using a comma-separated list of algorithms: -disco oligos,dyads', required=False)
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312 parser.add_argument('-source', '--sourceFile', metavar='<SOURCE_FILE>', type=str, nargs=1, help='Enter the source of the fasta sequence file. Supported source: galaxy', required=False)
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313 parser.add_argument('-verb', '--verbosity', metavar='<VERBOSITY>', type=int, nargs=1, help='Verbosity.', required=False)
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314 parser.add_argument('-ref_motif', '--ref_motif', metavar='<REF_MOTIF>', type=argparse.FileType('r'), nargs=1, help='Motif annotated in some transcription factor database (e.g. RegulonDB, Jaspar, TRANSFAC) for the transcription factor of interest.', required=False)
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315 parser.add_argument('-motif_db', '--motif_db', metavar='<MOTIF_DB>', type=str, nargs=1, help='Name of motif database.', required=False)
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316
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317 ################################ galaxy arguments ############################################################
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318 parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
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319 parser.add_argument('-outGalaxy2', '--outGalaxy2', metavar='<OUT_GALAXY2>', type=str, nargs=1, required=False)
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320 parser.add_argument('-server', '--server', metavar='<SERVEUR>', type=str, nargs=1, help='RSAT server', required=True)
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321 ###########################################################'
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322
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323 args = parser.parse_args()
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324
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325 ###########################################################
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326 ## Test arguments
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327
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328 fasta_test_file = args.test_file[0].read()
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329
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330 if not args.control_file is None :
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331 fasta_control_file = args.control_file[0].read()
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332 else :
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333 fasta_control_file =""
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334
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335 if not args.ref_motif is None :
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336 refMotifValue = args.ref_motif[0].read()
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337 else :
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338 refMotifValue =""
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339
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340 maxSeqLengthValue = testNone(args.maxSeqLength)
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341 maxMotifNumberValue = testNone(args.maxMotifNumber)
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342 topPeaksNumber = testNone(args.topPeaks)
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343 minLengthNumber = testNone(args.minLength)
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344 maxLengthNumber = testNone(args.maxLength)
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345 markovModelValue = testNone(args.markovModel)
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346 minMarkovValue = testNone(args.minMarkov)
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347 maxMarkovValue = testNone(args.maxMarkov)
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348 noovValue = testNone(args.noovDetection)
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349 classIntValue = testNone(args.classInt)
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350 strSummedValue = testNone(args.strSummed)
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351 graphTitleValue = testNone(args.graphTitle)
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352 imageFormatValue = testNone(args.imageFormat)
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353 discoAlgorithmValue = testNone(args.discoAlgorithm)
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354 sourceFileValue = testNone(args.sourceFile)
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355 verbosityValue = testNone(args.verbosity)
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356 motifdbValue = testNone(args.motif_db)
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357 outGalaxyValue = testNone(args.outGalaxy)
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358 outGalaxyValue2 = testNone(args.outGalaxy2)
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359 serverValue = testNone(args.server)
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360
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361 ###########################################################'
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362 ## Create the SOAP client to request the RSAT service
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363
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364 # Define URL for RSAT services
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365 url = serverDict[serverValue]
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366 print url
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367
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368 # Create the client
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369 client = Client(url)
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370
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371 # Need service interface to perform requests
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372 rsat_service = client.service
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373
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374 # Define client header
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375 userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
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376 peakMotifsVersion,
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377 os.path.basename( __file__ ),
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378 platform.python_version(),
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379 platform.system()
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380 )
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381
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382 httpHeaders = {'User-agent': userAgent}
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383 client.set_options(headers=httpHeaders)
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384 client.set_options(timeout=300)
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385
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386
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387 ###########################################################'
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388 ## Create request
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389 peakMotifsRequest = {
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390
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391 'test' : fasta_test_file,
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392 'control' : fasta_control_file,
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393 'max_seq_length' : maxSeqLengthValue,
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394 'max_motif_number' : maxMotifNumberValue,
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395 'top_peaks' : topPeaksNumber,
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396 'min_length' : minLengthNumber,
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397 'max_length' : maxLengthNumber,
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398 'markov' : markovModelValue,
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399 'min_markov' : minMarkovValue,
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400 'max_markov' : maxMarkovValue,
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401 'noov' : noovValue,
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402 'class_int' : classIntValue,
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403 'str' : strSummedValue,
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404 'graph_title' : graphTitleValue,
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405 'image_format' : imageFormatValue,
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406 'disco' : discoAlgorithmValue,
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407 'source' : sourceFileValue,
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408 'ref_motif' : refMotifValue,
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409 'verbosity' : verbosityValue,
|
|
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410 'motif_db' : motifdbValue
|
|
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411 #'output' : 'blablabla'
|
|
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412
|
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413 }
|
|
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414
|
|
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415
|
|
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416 ###########################################################'
|
|
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417 ## Run job in RSAT server
|
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418 result = call_run_service(rsat_service, peakMotifsRequest)
|
|
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419
|
|
|
420 #logFile = open("/bioinfo/users/jbrayet/Bureau/peak_motifs.log","w")
|
|
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421
|
|
|
422 #logFile.write("###############################################\n")
|
|
|
423 #logFile.write("Command performed on server\n")
|
|
|
424 #logFile.write(result.command)
|
|
|
425 #logFile.write("\n")
|
|
|
426 #logFile.write("###############################################\n")
|
|
|
427 #logFile.write("Result\n")
|
|
|
428 #logFile.write(result.server)
|
|
|
429
|
|
|
430 print("###############################################\n")
|
|
|
431 print("Command performed on server\n")
|
|
|
432 print(result.command)
|
|
|
433 print("\n")
|
|
|
434 print("###############################################\n")
|
|
|
435 print("Result\n")
|
|
|
436 print(result.server)
|
|
|
437
|
|
|
438 ###########################################################'
|
|
|
439 ## Build result URL
|
|
|
440
|
|
|
441 """
|
|
|
442 zipFileDict = {
|
|
|
443
|
|
|
444 "fr_ens":"http://protists.rsat.eu/rsat/",
|
|
|
445 "fr_mrs":"http://fungi.rsat.eu/rsat/",
|
|
|
446 "fr_ro":"http://metazoa.rsat.eu/",
|
|
|
447 "fr_mrs_2":"http://teaching.rsat.eu/rsat/",
|
|
|
448 "es":"http://plants.rsat.eu/rsat/",
|
|
|
449 "mx":"http://prokaryotes.rsat.eu/rsa-tools/"
|
|
|
450
|
|
|
451 }
|
|
|
452 """
|
|
|
453
|
|
|
454 nameFile = "peak-motifs_results.zip"
|
|
|
455 urlResult=buildZipUrl(result.server)
|
|
|
456 print urlResult
|
|
|
457
|
|
|
458 #ogFile.write("\n"+urlResult)
|
|
|
459
|
|
|
460 ###########################################################'
|
|
|
461 ## Wait RSAT server
|
|
|
462 while urllib.urlopen(urlResult).getcode() != 200:
|
|
|
463 #logFile.write(str(urllib.urlopen(urlResult).getcode())+"\n")
|
|
|
464 time.sleep(5)
|
|
|
465
|
|
|
466 #logFile.write(str(nameFile)+"\n")
|
|
50
|
467 #time.sleep(5)
|
|
2
|
468 #while urllib.urlretrieve(urlResult, nameFile)
|
|
|
469 #try:
|
|
|
470
|
|
50
|
471 folderName=recupRSATResult(urlResult,nameFile)
|
|
2
|
472
|
|
50
|
473 while(not(os.path.exists(folderName+"peak-motifs_synthesis.html"))):
|
|
|
474 os.popen("rm -rf "+folderName)
|
|
|
475 recupRSATResult(urlResult,nameFile)
|
|
2
|
476
|
|
|
477 #logFile.write("\n"+folderName+"\n")
|
|
|
478 #logFile.write("\n"+outGalaxyValue+"\n")
|
|
|
479
|
|
|
480 os.popen("cp "+folderName+"peak-motifs_synthesis.html "+outGalaxyValue)
|
|
|
481 os.popen("cp "+nameFile+" "+folderName)
|
|
|
482 #logFile.close()
|
|
|
483 #os.popen("sed -i \"1iHHEELLLOOO\" "+outGalaxyValue)
|
|
|
484 #os.popen("sed -i \"1i<style type=\'text/css\'></style>\" "+outGalaxyValue)
|
|
|
485
|
|
|
486 ###########################################################'
|
|
|
487 ##Create results folder name
|
|
|
488 outGalaxyValueDir = outGalaxyValue.replace(".dat","_files")
|
|
|
489
|
|
|
490 #logFile.write("\noutGalaxyValueDir : " +outGalaxyValueDir)
|
|
|
491
|
|
|
492 #logFile.close()
|
|
|
493
|
|
|
494 # Create results folder
|
|
|
495 os.popen("mkdir "+outGalaxyValueDir)
|
|
|
496
|
|
|
497 # Copy results files in results folder
|
|
|
498 os.popen("cp -R "+folderName+"data " + outGalaxyValueDir+"/data")
|
|
|
499 os.popen("cp -R "+folderName+"reports " + outGalaxyValueDir+"/reports")
|
|
|
500 os.popen("cp -R "+folderName+"results " + outGalaxyValueDir+"/results")
|
|
|
501
|
|
|
502 if not outGalaxyValue2 =="":
|
|
|
503 os.popen("cp "+folderName+"results/sites/peak-motifs_all_motifs_seqcoord.bed "+outGalaxyValue2)
|
|
|
504
|
|
|
505
|
|
|
506
|
|
|
507
|
|
|
508
|
|
|
509
|
|
|
510
|
