diff dyadAnalysis_wrapper.py @ 26:2f3462ac56aa draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dyadAnalysis_wrapper.py	Tue Sep 22 08:02:07 2015 -0400
@@ -0,0 +1,209 @@
+#! /usr/bin/python
+# -*- coding: utf8 -*-
+
+"""#dyad analysis soap - developed by Jocelyn Brayet <[e-mail]>
+#Copyright (C) 2015  Institut Curie
+#
+#This program is free software: you can redistribute it and/or modify
+#it under the terms of the GNU General Public License as published by
+#the Free Software Foundation, either version 3 of the License, or
+#(at your option) any later version.
+#
+#This program is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#GNU General Public License for more details.
+#
+#You should have received a copy of the GNU General Public License
+#along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+###########################################################'
+# 
+#Analysis of spaced dyads in a set of DNA sequences.
+#
+###########################################################'
+# 
+#usage: dyad-analysis_soap.py [-h] -sequence_file <SEQUENCE_FILE> -length
+#                             <LENGTH> -organism <ORGANISM> -spacing <SPACING>
+#                             [-stats <STATS>] [-type <TYPE>] -server <SERVEUR>
+#
+#optional arguments:
+#  -h, --help            show this help message and exit
+#  -sequence_file <SEQUENCE_FILE>, --sequence_file <SEQUENCE_FILE>
+#                        Input sequence (FASTA file).
+#  -length <LENGTH>, --length <LENGTH>
+#                        Dyad length.
+#  -organism <ORGANISM>, --organism <ORGANISM>
+#                        Organism.
+#  -spacing <SPACING>, --spacing <SPACING>
+#                        Spacing between elements of the dyads.
+#  -stats <STATS>, --stats <STATS>
+#                        List of statistics to return. Supported:occ, mseq,
+#                        freq, proba, ratio, zscore, like, pos, rank.
+#  -type <TYPE>, --type <TYPE>
+#                        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
+#  -server <SERVEUR>, --server <SERVEUR>
+#
+#Version 0.1 - 16/04/2015
+# 
+###########################################################'"""
+__author__ =  'Jocelyn Brayet'
+dyadAnalysisVersion = '0.1 - 16/04/2015'
+
+###########################################################'
+## Import
+
+import argparse
+import os
+import urllib
+from suds.client import Client
+import platform
+
+###########################################################'
+
+################################ functions ############################################################
+## Define a function to make a service perform the desired request using provided arguments
+def call_run_service(rsat_service, args):
+	"""
+	Run job in RSAT server.
+		service -> RSAT web service
+		args -> web service request
+	"""
+	
+	result = rsat_service.dyad_analysis(args)
+	return result
+
+def testNone(argument):
+	"""
+	Test if argument is None or not.
+		argument -> argument give by user
+	"""
+
+	if not argument is None:
+		variable = argument[0]
+	else:
+		variable = ""
+	return variable
+
+
+###########################################################'
+# server dictionary
+serverDict = {
+    
+    "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
+    "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
+    "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
+    "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
+    "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
+    "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
+    
+    }
+
+###########################################################'
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser(description='Analysis of spaced dyads in a set of DNA sequences.', epilog='Version '+dyadAnalysisVersion)
+
+    ########### compare matrices arguments ####################
+
+    parser.add_argument('-sequence_file', '--sequence_file', metavar='<SEQUENCE_FILE>', type=argparse.FileType('r'), nargs=1, help='Input sequence (FASTA file).', required=True)
+    parser.add_argument('-length', '--length', metavar='<LENGTH>', type=int, nargs=1, help='Dyad length.', required=True)
+    parser.add_argument('-organism', '--organism', metavar='<ORGANISM>', type=str, nargs=1, help='Organism.', required=True)
+    parser.add_argument('-spacing', '--spacing', metavar='<SPACING>', type=int, nargs=1, help='Spacing between elements of the dyads.', required=True)
+    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)
+    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)
+
+
+
+    ########### galaxy arguments ##############################
+    parser.add_argument('-server', '--server', metavar='<SERVEUR>', type=str, nargs=1, required=True)
+    parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
+    ###########################################################
+
+    args = parser.parse_args()
+
+    sequence_file = args.sequence_file[0].read()
+    serverValue = testNone(args.server)
+    length = testNone(args.length)
+    organism = testNone(args.organism)
+    spacing = testNone(args.spacing)
+    stats = testNone(args.stats)
+    typeValue = testNone(args.type)
+    outGalaxyValue = testNone(args.outGalaxy)
+
+    
+    ###########################################################'
+    ## Create the SOAP client to request the RSAT service
+    
+    
+    # Load Client class from suds
+    # Define URL for RSAT services 
+    url =  serverDict[serverValue]
+    # Create the client
+    client = Client(url)
+    
+    # Need service interface to perform requests
+    rsat_service = client.service
+    
+    #print client
+
+    # Define client header
+    userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
+        dyadAnalysisVersion, 
+        os.path.basename( __file__ ),
+        platform.python_version(), 
+        platform.system()
+    )
+    
+    httpHeaders = {'User-agent': userAgent}
+    client.set_options(headers=httpHeaders)
+    client.set_options(timeout=300)
+    
+
+    dyadAnalysisRequest = {
+        
+       	'output' : 'both',
+	'format' : 'fasta',
+	'sequence' : sequence_file,
+	'length' : length,
+	'organism' : organism,
+	'spacing' : spacing,
+	'stats' : stats,
+	'type' : typeValue
+
+    }
+
+      
+    result = call_run_service(rsat_service, dyadAnalysisRequest)
+
+    
+    print url
+
+    print "###############################################"
+    print "Command performed on server"
+    print result.command
+    print "###############################################"
+    print "Result"
+    print result.server    
+    
+    nameFile = "dyad_analysis_results.txt"
+    
+    urlResult=result.server.replace("$RSAT/public_html/",url.replace("web_services/RSATWS.wsdl",""))
+
+    print urlResult
+    
+    urllib.urlretrieve(urlResult, nameFile)
+
+
+    os.popen("cp "+nameFile+" "+outGalaxyValue)
+
+
+
+
+
+