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changeset 141:ff6607328942 draft

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Uploaded
author mzytnicki
date Fri, 10 Jan 2014 09:04:03 -0500
parents a7825a22f239
children 23ace8a3e22c
files SMART/Java/Python/CompareOverlappingAdapt.py SMART/Java/Python/CompareOverlappingSmallQuery.py SMART/Java/Python/CompareOverlappingSmallRef.py
diffstat 3 files changed, 131 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/CompareOverlappingAdapt.py	Fri Jan 10 09:04:03 2014 -0500
@@ -0,0 +1,115 @@
+#! /usr/bin/env python
+#
+# Copyright INRA-URGI 2009-2011
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+# 
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+from optparse import OptionParser
+import os.path
+from SMART.Java.Python.CompareOverlappingSmallQuery import CompareOverlappingSmallQuery
+from SMART.Java.Python.CompareOverlappingSmallRef import CompareOverlappingSmallRef
+from SMART.Java.Python.CompareOverlapping import CompareOverlapping
+
+
+MAX_SIZE = 10000000
+REFERENCE = 0
+QUERY = 1
+
+
+class CompareOverlappingAdapt(object):
+
+	def __init__(self, verbosity):
+		self.verbosity = verbosity
+
+	def setReferenceFile(self, fileName):
+		self.refSize = os.path.getsize(fileName)
+		print "refsize:", self.refSize
+
+	def setQueryFile(self, fileName):
+		self.querySize = os.path.getsize(fileName)
+		print "querysize:", self.querySize
+
+	def run(self, options):
+		object = None
+		if self.refSize < MAX_SIZE:
+			if self.verbosity >= 100:
+				print "Using 'Compare Overlapping Small Reference'"
+			object = CompareOverlappingSmallQuery(options.verbosity)
+		elif self.querySize < MAX_SIZE:
+			if self.verbosity >= 100:
+				print "Using 'Compare Overlapping Small Query'"
+			object = CompareOverlappingSmallRef(options.verbosity)
+		if object != None:
+			object.setQueryFile(options.inputFileName1, options.format1)
+			object.setReferenceFile(options.inputFileName2, options.format2)
+			object.setOutputFile(options.outputFileName)
+			object.includeNotOverlapping(options.notOverlapping)
+			object.setDistance(options.distance)
+			object.setCollinear(options.collinear)
+			object.setAntisense(options.antisense)
+			object.setInvert(options.exclude)
+			object.setMinOverlap(options.minOverlap)
+			object.run()
+			return
+		if self.verbosity >= 100:
+			print "Using 'Compare Overlapping'"
+		object = CompareOverlapping(options.verbosity)
+		object.setInput(options.inputFileName1, options.format1, QUERY)
+		object.setInput(options.inputFileName2, options.format2, REFERENCE)
+		object.setOutput(options.outputFileName)
+		object.getAntisenseOnly(options.antisense)
+		object.getColinearOnly(options.collinear)
+		object.getInvert(options.exclude)
+		object.setMaxDistance(options.distance)
+		object.includeNotOverlapping(options.notOverlapping)
+		object.setMinOverlap(options.minOverlap)
+		object.run()
+
+
+if __name__ == "__main__":
+	
+	description = "Compare Overlapping Adapt v1.0.1: Start the relevant CompareOverlappingX depending on the input data. [Category: Data Comparison]"
+
+	parser = OptionParser(description = description)
+	parser.add_option("-i", "--input1",	        dest="inputFileName1", action="store",			           type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
+	parser.add_option("-f", "--format1",        dest="format1",		  action="store",			           type="string", help="format of previous file [compulsory] [format: transcript file format]")
+	parser.add_option("-j", "--input2",	        dest="inputFileName2", action="store",			           type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
+	parser.add_option("-g", "--format2",        dest="format2",		  action="store",			           type="string", help="format of previous file [compulsory] [format: transcript file format]")
+	parser.add_option("-o", "--output",	        dest="outputFileName", action="store",			           type="string", help="output file [format: output file in GFF3 format]")
+	parser.add_option("-O", "--notOverlapping", dest="notOverlapping", action="store_true", default=False,				 help="also output not overlapping data [format: bool] [default: false]")
+	parser.add_option("-d", "--distance",		dest="distance",	   action="store",	    default=0,	   type="int",	 help="accept some distance between query and reference [format: int]")
+	parser.add_option("-c", "--collinear",		dest="collinear",	   action="store_true", default=False,			 	 help="provide collinear features [format: bool] [default: false]")
+	parser.add_option("-a", "--antisense",		dest="antisense",	   action="store_true", default=False,			 	 help="provide antisense features [format: bool] [default: false]")
+	parser.add_option("-x", "--exclude",		dest="exclude",		   action="store_true", default=False,			 	 help="invert the match [format: bool] [default: false]")
+	parser.add_option("-m", "--minOverlap",  	dest="minOverlap",     action="store",      default=False, type="int",   help="min. # overlap between query and reference [format: bool] [default: false]")
+	parser.add_option("-v", "--verbosity",      dest="verbosity",	   action="store",      default=1,     type="int",	 help="trace level [format: int]")
+	(options, args) = parser.parse_args()
+
+	coa = CompareOverlappingAdapt(options.verbosity)
+	coa.setQueryFile(options.inputFileName1)
+	coa.setReferenceFile(options.inputFileName2)
+	coa.run(options)
--- a/SMART/Java/Python/CompareOverlappingSmallQuery.py	Tue Nov 05 05:52:22 2013 -0500
+++ b/SMART/Java/Python/CompareOverlappingSmallQuery.py	Fri Jan 10 09:04:03 2014 -0500
@@ -74,6 +74,7 @@
 		self.collinear      = False
 		self.pcOverlapQuery = False
 		self.pcOverlapRef   = False
+		self.minOverlap     = False
 		self.bins	        = {}
 		self.overlaps       = {}
 		self.notOverlapping = False
@@ -107,6 +108,9 @@
 		self.pcOverlapQuery = pcOverlapQuery
 		self.pcOverlapRef   = pcOverlapRef
 
+	def setMinOverlap(self, minOverlap):
+		self.minOverlap = minOverlap
+
 	def includeNotOverlapping(self, boolean):
 		self.notOverlapping = boolean
 
@@ -135,6 +139,8 @@
 			return False
 		if self.antisense and queryTranscript.getDirection() == refTranscript.getDirection():
 			return False
+		if self.minOverlap and not queryTranscript.overlapWithExon(refTranscript, self.minOverlap):
+			return False
 		querySize = queryTranscript.getSize()
 		if self.pcOverlapQuery and not queryTranscript.overlapWithExon(refTranscript, int(querySize * self.pcOverlapQuery / 100.0)):
 			return False
@@ -223,6 +229,7 @@
 	parser.add_option("-a", "--antisense",		dest="antisense",	   action="store_true", default=False,			 	 help="provide antisense features [format: bool] [default: false]")
 	parser.add_option("-p", "--pcOverlapQuery",	dest="pcOverlapQuery", action="store",      default=False, type="int",	 help="min. % overlap of the query [format: bool] [default: false]")
 	parser.add_option("-P", "--pcOverlapRef",	dest="pcOverlapRef",   action="store",      default=False, type="int",   help="min. % overlap of the reference [format: bool] [default: false]")
+	parser.add_option("-m", "--minOverlap",  	dest="minOverlap",     action="store",      default=False, type="int",   help="min. # overlap between query and reference [format: bool] [default: false]")
 	parser.add_option("-x", "--exclude",		dest="exclude",		   action="store_true", default=False,			 	 help="invert the match [format: bool] [default: false]")
 	parser.add_option("-v", "--verbosity",      dest="verbosity",	   action="store",      default=1,     type="int",	 help="trace level [format: int]")
 	(options, args) = parser.parse_args()
@@ -236,5 +243,6 @@
 	cosq.setCollinear(options.collinear)
 	cosq.setAntisense(options.antisense)
 	cosq.setMinPercentOverlap(options.pcOverlapQuery, options.pcOverlapRef)
+	cosq.setMinOverlap(options.minOverlap)
 	cosq.setInvert(options.exclude)
 	cosq.run()
--- a/SMART/Java/Python/CompareOverlappingSmallRef.py	Tue Nov 05 05:52:22 2013 -0500
+++ b/SMART/Java/Python/CompareOverlappingSmallRef.py	Fri Jan 10 09:04:03 2014 -0500
@@ -74,6 +74,7 @@
 		self.distance       = None
 		self.pcOverlapQuery = False
 		self.pcOverlapRef   = False
+		self.minOverlap     = False
 		self.bins	        = {}
 		self.notOverlapping = False
 
@@ -106,6 +107,9 @@
 		self.pcOverlapQuery = pcOverlapQuery
 		self.pcOverlapRef   = pcOverlapRef
 
+	def setMinOverlap(self, minOverlap):
+		self.minOverlap = minOverlap
+
 	def includeNotOverlapping(self, boolean):
 		self.notOverlapping = boolean
 
@@ -139,6 +143,8 @@
 			return False
 		if self.antisense and queryTranscript.getDirection() == refTranscript.getDirection():
 			return False
+		if self.minOverlap and not queryTranscript.overlapWithExon(refTranscript, self.minOverlap):
+			return False
 		querySize = queryTranscript.getSize()
 		if self.pcOverlapQuery and not queryTranscript.overlapWithExon(refTranscript, int(querySize * self.pcOverlapQuery / 100.0)):
 			return False
@@ -217,6 +223,7 @@
 	parser.add_option("-a", "--antisense",		dest="antisense",	   action="store_true", default=False,			 	 help="provide antisense features [format: bool] [default: false]")
 	parser.add_option("-p", "--pcOverlapQuery",	dest="pcOverlapQuery", action="store",      default=False, type="int",	 help="min. % overlap of the query [format: bool] [default: false]")
 	parser.add_option("-P", "--pcOverlapRef",	dest="pcOverlapRef",   action="store",      default=False, type="int",   help="min. % overlap of the reference [format: bool] [default: false]")
+	parser.add_option("-m", "--minOverlap",  	dest="minOverlap",     action="store",      default=False, type="int",   help="min. # overlap between query and reference [format: bool] [default: false]")
 	parser.add_option("-x", "--exclude",		dest="exclude",		   action="store_true", default=False,			 	 help="invert the match [format: bool] [default: false]")
 	parser.add_option("-v", "--verbosity",      dest="verbosity",	   action="store",      default=1,     type="int",	 help="trace level [format: int]")
 	(options, args) = parser.parse_args()
@@ -230,5 +237,6 @@
 	cosr.setAntisense(options.antisense)
 	cosr.setInvert(options.exclude)
 	cosr.setMinPercentOverlap(options.pcOverlapQuery, options.pcOverlapRef)
+	cosr.setMinOverlap(options.minOverlap)
 	cosr.run()