diff peakMotifs_wrapper.py @ 2:dce9495ac542 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peakMotifs_wrapper.py	Tue Sep 22 05:15:21 2015 -0400
@@ -0,0 +1,496 @@
+#! /usr/bin/python
+# -*- coding: utf8 -*-
+"""#Peak Motifs - 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/>.
+#
+###########################################################'
+# 
+#Client to download peak-motifs results from RSAT server.
+#
+#
+#usage: peak-motifs_soap.py [-h] -test <TEST_FILE> [-control <CONTROL_FILE>]
+#				[-max_seq_length <MAX_SEQ_LENGTH>]
+#				[-max_motif_number <MAX_MOTIF_NUMBER>]
+#				[-top_peaks <TOP_PEAKS>] [-min_length <MIN_LENGTH>]
+#				[-max_length <MAX_LENGTH>] [-markov <MARKOV_MODEL>]
+#				[-min_markov <MIN_MARKOV>]
+#				[-max_markov <MAX_MARKOV>] [-noov <NOOV_DETECTION>]
+#				[-class_int <CLASS_INT>] [-str <STR_SUMMED>]
+#				[-graph_title <GRAPH_TITLE>]
+#				[-image_format <IMAGE_FORMAT>]
+#				[-disco [<DISCO_ALGORITHM> [<DISCO_ALGORITHM> ...]]]
+#				[-source <SOURCE_FILE>] [-verb <VERBOSITY>]
+#				[-ref_motif <REF_MOTIF>] -server <SERVEUR>
+#
+#optional arguments:
+#  -h, --help		show this help message and exit
+#  -test <TEST_FILE>, --test_file <TEST_FILE>
+#			Input test peak sequence in fasta format.
+#  -control <CONTROL_FILE>, --control_file <CONTROL_FILE>
+#			Input control peak sequence in fasta format.
+#  -max_seq_length <MAX_SEQ_LENGTH>, --maxSeqLength <MAX_SEQ_LENGTH>
+#			Maximal sequence length.
+#  -max_motif_number <MAX_MOTIF_NUMBER>, --maxMotifNumber <MAX_MOTIF_NUMBER>
+#			Maximal number of motifs (matrices) to return for
+#			pattern discovery algorithms.
+#  -top_peaks <TOP_PEAKS>, --topPeaks <TOP_PEAKS>
+#			Restrict the analysis to the N peaks at the top of the
+#			input sequence file.
+#  -min_length <MIN_LENGTH>, --minLength <MIN_LENGTH>
+#			Minimal oligonucleotide length.
+#  -max_length <MAX_LENGTH>, --maxLength <MAX_LENGTH>
+#			Maximal oligonucleotide length.
+#  -markov <MARKOV_MODEL>, --markovModel <MARKOV_MODEL>
+#			Order of the Markov model used to estimatd expected
+#			oligonucleotide frequencies for oligo-analysis and
+#			local-word-analysis.
+#  -min_markov <MIN_MARKOV>, --minMarkov <MIN_MARKOV>
+#			Minimal value for markov order. Use in combination
+#			with the next option (max_markov).
+#  -max_markov <MAX_MARKOV>, --maxMarkov <MAX_MARKOV>
+#			Maximal value for markov order. Use in combination
+#			with the previous option (min_markov).
+#  -noov <NOOV_DETECTION>, --noovDetection <NOOV_DETECTION>
+#			No overlapping of oligos allowed if value = 1.
+#  -class_int <CLASS_INT>, --classInt <CLASS_INT>
+#			Class interval for position-analysis. The width of the
+#			position classes, in number of bases (default: 20).
+#  -str <STR_SUMMED>, --strSummed <STR_SUMMED>
+#			Oligonucleotide occurrences found on both stands are
+#			summed (2) or not (1). Default is 2.
+#  -graph_title <GRAPH_TITLE>, --graphTitle <GRAPH_TITLE>
+#			Title displayed on top of the graphs.
+#  -image_format <IMAGE_FORMAT>, --imageFormat <IMAGE_FORMAT>
+#			Image format. All the formats supported by XYgraph can
+#			be used.
+#  -disco [<DISCO_ALGORITHM> [<DISCO_ALGORITHM> ...]], --discoAlgorithm [<DISCO_ALGORITHM> [<DISCO_ALGORITHM> ...]]
+#			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
+#  -source <SOURCE_FILE>, --sourceFile <SOURCE_FILE>
+#			Enter the source of the fasta sequence file. Supported
+#			source: galaxy
+#  -verb <VERBOSITY>, --verbosity <VERBOSITY>
+#			Verbosity.
+#  -ref_motif <REF_MOTIF>, --ref_motif <REF_MOTIF>
+#			Motif annotated in some transcription factor database
+#			(e.g. RegulonDB, Jaspar, TRANSFAC) for the
+#			transcription factor of interest.
+#  -server <SERVEUR>, --server <SERVEUR>
+#			RSAT server
+#  -outGalaxy <OUT_GALAXY>, --outGalaxy <OUT_GALAXY>
+#
+#Version 0.1 - 30/01/2015 - Adapted from Jocelyn Brayet, France Genomique team
+#
+###########################################################"""
+__author__ =  'Jocelyn Brayet'
+
+###########################################################'
+## Import
+
+import argparse
+import os
+import urllib
+import zipfile
+import time
+import platform
+from suds.client import Client
+
+###########################################################'
+
+###########################################################'
+## Define log options for suds
+
+# Import log package
+#import logging
+
+# Import log package
+#import logging
+# création de l'objet logger qui va nous servir à écrire dans les logs
+#logger = logging.getLogger()
+# on met le niveau du logger à DEBUG, comme ça il écrit tout
+#logger.setLevel(logging.DEBUG)
+# Configure log of suds clients to DEBUG for verbose output concerning Client request
+#logging.getLogger('suds.client').setLevel(logging.ERROR)
+#logging.getLogger('suds.transport').setLevel(logging.ERROR)
+#logging.getLogger('suds.xsd.schema').setLevel(logging.ERROR)
+#logging.getLogger('suds.wsdl').setLevel(logging.ERROR)
+
+
+# création d'un second handler qui va rediriger chaque écriture de log
+# sur la console
+#steam_handler = logging.StreamHandler()
+#steam_handler.setLevel(logging.DEBUG)
+#logger.addHandler(steam_handler)
+
+#logger.info('Hello')
+
+#print(client.factory.create('peak_motifs'))
+
+#	  (PeakMotifsRequest){
+#		 output = None -> ok
+#		 verbosity = None
+#		 test = None -> ok
+#		 tmp_test_infile = None
+#		 control = None
+#		 tmp_control_infile = None
+#		 max_seq_length = None
+#		 max_motif_number = None
+#		 ref_motif = None
+#		 top_peaks = None
+#		 min_length = None
+#		 max_length = None
+#		 markov = None
+#		 min_markov = None
+#		 max_markov = None
+#		 noov = None
+#		 class_int = None
+#		 str = None
+#		 graph_title = None
+#		 image_format = None
+#		 disco = None
+#		 source = None
+#		 task = None
+#	  }
+# }
+
+
+################################ functions ############################################################
+## Define a function to make a service perform the desired request using provided arguments
+def call_run_service(service, args):
+	"""
+	Run job in RSAT server.
+		service -> RSAT web service
+		args -> web service request 	 
+	"""
+	
+	result = rsat_service.peak_motifs(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
+
+
+###########################################################'
+## Function to recup results
+
+def buildZipUrl(algoResults):
+	"""
+	Recup results give by RSAT server.
+		algoResults -> result give by RSAT server
+	"""
+	
+	recupResult = str(algoResults)
+	tabResults=recupResult.split("\n")
+	urlZip = tabResults[4].replace("\t","")
+				
+	return urlZip
+
+
+## Tested with python 2.6.6
+peakMotifsVersion = '0.1 - 30/01/2015'
+
+###########################################################'
+# server dictionary
+serverDict = {
+
+	"fr_ens":"http://rsat01.biologie.ens.fr/rsat/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"
+
+	}
+
+"""
+serverDict = {
+
+	"fr_ens":"http://protists.rsat.eu/rsat/web_services/RSATWS.wsdl",
+	"fr_mrs":"http://fungi.rsat.eu/rsat/web_services/RSATWS.wsdl",
+	"fr_ro":"http://metazoa.rsat.eu/web_services/RSATWS.wsdl",
+	"fr_mrs_2":"http://teaching.rsat.eu/rsat/web_services/RSATWS.wsdl",
+	"es":"http://plants.rsat.eu/rsat/web_services/RSATWS.wsdl",
+	"mx":"http://prokaryotes.rsat.eu/rsa-tools/web_services/RSATWS.wsdl"
+	
+	}
+"""
+
+if __name__ == '__main__':
+
+	########### peak motifs arguments ####################
+	parser = argparse.ArgumentParser(description='Client to download peak-motifs results from RSAT server.', epilog='Version '+peakMotifsVersion)
+	
+	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)
+	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)
+	parser.add_argument('-max_seq_length', '--maxSeqLength', metavar='<MAX_SEQ_LENGTH>', type=int, nargs=1, help='Maximal sequence length.', required=False)
+	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)
+	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)
+	parser.add_argument('-min_length', '--minLength', metavar='<MIN_LENGTH>', type=int, nargs=1, help='Minimal oligonucleotide length.', required=False)
+	parser.add_argument('-max_length', '--maxLength', metavar='<MAX_LENGTH>', type=int, nargs=1, help='Maximal oligonucleotide length.', required=False)
+	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)
+	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)
+	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)
+	parser.add_argument('-noov', '--noovDetection', metavar='<NOOV_DETECTION>', type=int, nargs=1, help='No overlapping of oligos allowed if value = 1.', required=False)
+	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)
+	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)
+	parser.add_argument('-graph_title', '--graphTitle', metavar='<GRAPH_TITLE>', type=str, nargs=1, help='Title displayed on top of the graphs.', required=False)
+	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)
+	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)
+	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)
+	parser.add_argument('-verb', '--verbosity', metavar='<VERBOSITY>', type=int, nargs=1, help='Verbosity.', required=False)
+	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)
+	parser.add_argument('-motif_db', '--motif_db', metavar='<MOTIF_DB>', type=str, nargs=1, help='Name of motif database.', required=False)
+
+	################################ galaxy arguments ############################################################
+	parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
+        parser.add_argument('-outGalaxy2', '--outGalaxy2', metavar='<OUT_GALAXY2>', type=str, nargs=1, required=False)
+	parser.add_argument('-server', '--server', metavar='<SERVEUR>', type=str, nargs=1, help='RSAT server', required=True)
+	###########################################################'
+
+	args = parser.parse_args()
+
+	###########################################################
+	## Test arguments
+
+	fasta_test_file = args.test_file[0].read()
+	
+	if not args.control_file is None :
+		fasta_control_file = args.control_file[0].read()
+	else :
+		fasta_control_file =""
+   
+	if not args.ref_motif is None :
+		refMotifValue = args.ref_motif[0].read()
+	else :
+		refMotifValue =""
+
+	maxSeqLengthValue = testNone(args.maxSeqLength)
+	maxMotifNumberValue = testNone(args.maxMotifNumber)
+	topPeaksNumber = testNone(args.topPeaks)
+	minLengthNumber = testNone(args.minLength)
+	maxLengthNumber = testNone(args.maxLength)
+	markovModelValue = testNone(args.markovModel)
+	minMarkovValue = testNone(args.minMarkov)
+	maxMarkovValue = testNone(args.maxMarkov)
+	noovValue = testNone(args.noovDetection)
+	classIntValue = testNone(args.classInt)
+	strSummedValue = testNone(args.strSummed)
+	graphTitleValue = testNone(args.graphTitle)
+	imageFormatValue = testNone(args.imageFormat)
+	discoAlgorithmValue = testNone(args.discoAlgorithm)
+	sourceFileValue = testNone(args.sourceFile)
+	verbosityValue = testNone(args.verbosity)
+	motifdbValue = testNone(args.motif_db)
+	outGalaxyValue = testNone(args.outGalaxy)
+        outGalaxyValue2 = testNone(args.outGalaxy2)
+	serverValue = testNone(args.server)
+
+	###########################################################'
+	## Create the SOAP client to request the RSAT service
+
+	# Define URL for RSAT services 
+	url =  serverDict[serverValue]
+	print url
+
+	# Create the client
+	client = Client(url)
+
+	# Need service interface to perform requests
+	rsat_service = client.service
+
+	# Define client header
+	userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
+		peakMotifsVersion, 
+		os.path.basename( __file__ ),
+		platform.python_version(), 
+		platform.system()
+	)
+
+	httpHeaders = {'User-agent': userAgent}
+	client.set_options(headers=httpHeaders)
+	client.set_options(timeout=300)
+
+
+	###########################################################'
+	## Create request
+	peakMotifsRequest = {
+	
+		'test' : fasta_test_file,
+		'control' : fasta_control_file,
+		'max_seq_length' : maxSeqLengthValue,
+		'max_motif_number' : maxMotifNumberValue,
+		'top_peaks' : topPeaksNumber,
+		'min_length' : minLengthNumber,
+		'max_length' : maxLengthNumber,
+		'markov' : markovModelValue,
+		'min_markov' : minMarkovValue,
+		'max_markov' : maxMarkovValue,
+		'noov' : noovValue,
+		'class_int' : classIntValue,
+		'str' : strSummedValue,
+		'graph_title' : graphTitleValue,
+		'image_format' : imageFormatValue,
+		'disco' : discoAlgorithmValue,
+		'source' : sourceFileValue,
+		'ref_motif' : refMotifValue,
+		'verbosity' : verbosityValue,
+		'motif_db' : motifdbValue
+		#'output' : 'blablabla'
+	
+	}
+
+
+	###########################################################'
+	## Run job in RSAT server
+	result = call_run_service(rsat_service, peakMotifsRequest)
+
+	#logFile = open("/bioinfo/users/jbrayet/Bureau/peak_motifs.log","w")
+
+	#logFile.write("###############################################\n")
+	#logFile.write("Command performed on server\n")
+	#logFile.write(result.command)
+	#logFile.write("\n")
+	#logFile.write("###############################################\n")
+	#logFile.write("Result\n")
+	#logFile.write(result.server)
+
+	print("###############################################\n")
+	print("Command performed on server\n")
+	print(result.command)
+	print("\n")
+	print("###############################################\n")
+	print("Result\n")
+	print(result.server)
+
+	###########################################################'
+	## Build result URL
+
+	"""
+	zipFileDict = {
+	
+		"fr_ens":"http://protists.rsat.eu/rsat/",
+		"fr_mrs":"http://fungi.rsat.eu/rsat/",
+		"fr_ro":"http://metazoa.rsat.eu/",
+		"fr_mrs_2":"http://teaching.rsat.eu/rsat/",
+		"es":"http://plants.rsat.eu/rsat/",
+		"mx":"http://prokaryotes.rsat.eu/rsa-tools/"
+	
+		}
+	"""
+
+	nameFile = "peak-motifs_results.zip"
+	urlResult=buildZipUrl(result.server)
+	print urlResult
+
+	#ogFile.write("\n"+urlResult)
+
+	###########################################################'
+	## Wait RSAT server
+	while urllib.urlopen(urlResult).getcode() != 200:
+	#logFile.write(str(urllib.urlopen(urlResult).getcode())+"\n")
+		time.sleep(5)
+
+	#logFile.write(str(nameFile)+"\n")
+
+	#while urllib.urlretrieve(urlResult, nameFile) 
+	#try:
+	###########################################################'
+	## Download RSAT results
+	urllib.urlretrieve(urlResult, nameFile)
+	#except IOError:
+	#logFile.write("\nResult URL is false")
+	#Logger.error("Result URL is false")
+
+
+	#logFile.write("\n"+nameFile+"\n")
+
+	###########################################################'
+	## Decompress results
+	#try:
+	zfile = zipfile.ZipFile(nameFile, 'r')
+	#except IOError:
+	#logFile.write("No zip file")
+	#Logger.error("No zip file")
+
+	tempflag = 0
+	folderName =""
+
+	for i in zfile.namelist():  ## On parcourt l'ensemble des fichiers de l'archive
+	
+		#logFile.write(i+"\n")
+		###############################
+			if tempflag ==0:
+				folderName = i
+		
+			tempflag = 1
+		###############################
+		
+			if i.endswith('/'):   ## S'il s'agit d'un repertoire, on se contente de creer le dossier 
+				os.makedirs(i)
+			else: 
+				data = zfile.read(i)	## lecture du fichier compresse 
+				fp = open(i, "wb")	  ## creation en local du nouveau fichier 
+				fp.write(data)		  ## ajout des donnees du fichier compresse dans le fichier local 
+				fp.close() 
+	zfile.close()
+
+	#logFile.write("\n"+folderName+"\n")
+	#logFile.write("\n"+outGalaxyValue+"\n")
+
+        os.popen("cp "+folderName+"peak-motifs_synthesis.html "+outGalaxyValue)
+	os.popen("cp "+nameFile+" "+folderName)
+        #logFile.close()
+        #os.popen("sed -i \"1iHHEELLLOOO\" "+outGalaxyValue)
+        #os.popen("sed -i \"1i<style type=\'text/css\'></style>\" "+outGalaxyValue)
+
+        ###########################################################'
+        ##Create results folder name
+        outGalaxyValueDir = outGalaxyValue.replace(".dat","_files")
+
+        #logFile.write("\noutGalaxyValueDir : " +outGalaxyValueDir)
+
+        #logFile.close()
+
+        # Create results folder
+        os.popen("mkdir "+outGalaxyValueDir)
+
+        # Copy results files in results folder
+        os.popen("cp -R "+folderName+"data " + outGalaxyValueDir+"/data")
+        os.popen("cp -R "+folderName+"reports " + outGalaxyValueDir+"/reports")
+        os.popen("cp -R "+folderName+"results " + outGalaxyValueDir+"/results")
+        
+        if not outGalaxyValue2 =="":
+            os.popen("cp "+folderName+"results/sites/peak-motifs_all_motifs_seqcoord.bed "+outGalaxyValue2)
+        
+        
+        
+
+
+
+