|
29
|
1 #! /usr/bin/python
|
|
|
2 # -*- coding: utf8 -*-
|
|
|
3 """#Compare Matrices - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
|
|
|
4 #Copyright (C) 2015 Institut Curie
|
|
|
5 #
|
|
|
6 #This program is free software: you can redistribute it and/or modify
|
|
|
7 #it under the terms of the GNU General Public License as published by
|
|
|
8 #the Free Software Foundation, either version 3 of the License, or
|
|
|
9 #(at your option) any later version.
|
|
|
10 #
|
|
|
11 #This program is distributed in the hope that it will be useful,
|
|
|
12 #but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
|
13 #MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
|
14 #GNU General Public License for more details.
|
|
|
15 #
|
|
|
16 #You should have received a copy of the GNU General Public License
|
|
|
17 #along with this program. If not, see <http://www.gnu.org/licenses/>.
|
|
|
18 #
|
|
|
19 ###########################################################'
|
|
|
20 #
|
|
|
21 #Client to download compare matrices results from RSAT server.
|
|
|
22 #
|
|
|
23 ###########################################################'"""
|
|
|
24
|
|
|
25 __author__ = 'Jocelyn Brayet'
|
|
|
26 compareMatricesVersion = '0.1 - 14/04/2015'
|
|
|
27
|
|
|
28
|
|
|
29 ###########################################################'
|
|
|
30 ## Import
|
|
|
31
|
|
|
32 import argparse
|
|
|
33 import os
|
|
|
34 import urllib
|
|
|
35 from suds.client import Client
|
|
|
36 import platform
|
|
|
37
|
|
|
38 ###########################################################'
|
|
|
39
|
|
|
40 ################################ functions ############################################################
|
|
|
41 ## Define a function to make a service perform the desired request using provided arguments
|
|
|
42 def call_run_service(service, args):
|
|
|
43 """
|
|
|
44 Run job in RSAT server.
|
|
|
45 service -> RSAT web service
|
|
|
46 args -> web service request
|
|
|
47 """
|
|
|
48
|
|
|
49 result = rsat_service.compare_matrices(args)
|
|
|
50 return result
|
|
|
51
|
|
|
52 def testNone(argument):
|
|
|
53 """
|
|
|
54 Test if argument is None or not.
|
|
|
55 argument -> argument give by user
|
|
|
56 """
|
|
|
57
|
|
|
58 if not argument is None:
|
|
|
59 variable = argument[0]
|
|
|
60 else:
|
|
|
61 variable = ""
|
|
|
62 return variable
|
|
|
63
|
|
|
64 ###########################################################'
|
|
|
65 # server dictionary
|
|
|
66 serverDict = {
|
|
|
67
|
|
|
68 "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
|
|
|
69 "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
|
|
|
70 "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
|
|
|
71 "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
|
|
|
72 "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
|
|
|
73 "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
|
|
|
74
|
|
|
75 }
|
|
|
76
|
|
|
77 ###########################################################'
|
|
|
78
|
|
|
79
|
|
|
80 if __name__ == '__main__':
|
|
|
81
|
|
|
82 parser = argparse.ArgumentParser(description='Client to download compare matrices results from RSAT server.', epilog='Version '+compareMatricesVersion)
|
|
|
83
|
|
|
84
|
|
|
85 ########### compare matrices arguments ####################
|
|
|
86
|
|
|
87 parser.add_argument('-matrix_1', '--matrix_1', metavar='<MATRIX_1>', type=argparse.FileType('r'), nargs=1, help='The first input containing one or several matrices.', required=True)
|
|
|
88 parser.add_argument('-matrix_2', '--matrix_2', metavar='<MATRIX_2>', type=argparse.FileType('r'), nargs=1, help='The second input containing one or several matrices.', required=True)
|
|
|
89 parser.add_argument('-format1', '--format1', metavar='<FORMAT_1>', type=str, nargs=1, help='Martix format for the first input. Supported fields: tab, cb, consensus, gibbs, meme, assembly.', required=True)
|
|
|
90 parser.add_argument('-format2', '--format2', metavar='<FORMAT_2>', type=str, nargs=1, help='Martix format for the second input. Supported fields: tab, cb, consensus, gibbs, meme, assembly.', required=True)
|
|
|
91 parser.add_argument('-returnResults', '--returnResults', metavar='<RETURN_RESULTS>', type=str, nargs=1, help='List of fields to return (only valid for the formats "profiles" and "matches").', required=False)
|
|
|
92 #parser.add_argument('-rc', '--rc', metavar='<RC>', type=int, nargs=1, help='Convert the matrix to its reverse complement if value = 1.', required=False)
|
|
|
93 #parser.add_argument('-decimals', '--decimals', metavar='<DECIMALS>', type=int, nargs=1, help='Number of decimals to print for real matrices (frequencies, weights, information) or to compute score distributions.', required=False)
|
|
|
94
|
|
|
95 ########### galaxy arguments ##############################
|
|
|
96 parser.add_argument('-server', '--server', metavar='<SERVEUR>', type=str, nargs=1, required=True)
|
|
|
97 parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
|
|
|
98 ###########################################################
|
|
|
99
|
|
|
100 args = parser.parse_args()
|
|
|
101
|
|
|
102 matrix_1 = args.matrix_1[0].read()
|
|
|
103 matrix_2 = args.matrix_2[0].read()
|
|
|
104 serverValue = testNone(args.server)
|
|
|
105 format1 = testNone(args.format1)
|
|
|
106 format2 = testNone(args.format2)
|
|
|
107 returnValue = testNone(args.returnResults)
|
|
|
108 outGalaxyValue = testNone(args.outGalaxy)
|
|
|
109 #returnTypeValue = testNone(args.return_type)
|
|
|
110 #permValue = testNone(args.perm)
|
|
|
111 #rcValue = testNone(args.rc)
|
|
|
112 #decimalsValue = testNone(args.decimals)
|
|
|
113
|
|
|
114 ###########################################################'
|
|
|
115 ## Create the SOAP client to request the RSAT service
|
|
|
116
|
|
|
117
|
|
|
118 # Load Client class from suds
|
|
|
119 # Define URL for RSAT services
|
|
|
120 url = serverDict[serverValue]
|
|
|
121 # Create the client
|
|
|
122 client = Client(url)
|
|
|
123
|
|
|
124 # Need service interface to perform requests
|
|
|
125 rsat_service = client.service
|
|
|
126
|
|
|
127 #print client
|
|
|
128
|
|
|
129 # Define client header
|
|
|
130 userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
|
|
|
131 compareMatricesVersion,
|
|
|
132 os.path.basename( __file__ ),
|
|
|
133 platform.python_version(),
|
|
|
134 platform.system()
|
|
|
135 )
|
|
|
136
|
|
|
137 httpHeaders = {'User-agent': userAgent}
|
|
|
138 client.set_options(headers=httpHeaders)
|
|
|
139 client.set_options(timeout=300)
|
|
|
140
|
|
|
141
|
|
|
142 compareMatricesRequest = {
|
|
|
143
|
|
|
144 'output' : 'both',
|
|
|
145 'matrix_1' : matrix_1,
|
|
|
146 'matrix_2' : matrix_2,
|
|
|
147 'format1' : format1,
|
|
|
148 'format2' : format2,
|
|
|
149 'return' : returnValue
|
|
|
150
|
|
|
151 }
|
|
|
152
|
|
|
153
|
|
|
154 result = call_run_service(rsat_service, compareMatricesRequest)
|
|
|
155
|
|
|
156
|
|
|
157 print url
|
|
|
158
|
|
|
159 print "###############################################"
|
|
|
160 print "Command performed on server"
|
|
|
161 print result.command
|
|
|
162 print "###############################################"
|
|
|
163 print "Result"
|
|
|
164 print result.server
|
|
|
165
|
|
|
166 nameFile = "test_compare_matrices"
|
|
|
167
|
|
|
168 urlResult=result.server.replace("$RSAT/public_html/",url.replace("web_services/RSATWS.wsdl",""))+"/.tab"
|
|
|
169
|
|
|
170 urllib.urlretrieve(urlResult, nameFile)
|
|
|
171
|
|
|
172 os.popen("cp "+nameFile+" "+outGalaxyValue)
|
|
|
173
|
|
|
174
|
|
|
175
|
|
|
176
|
|
|
177
|
