# HG changeset patch
# User m-zytnicki
# Date 1389362363 18000
# Node ID 2ac71607aa60bfdbbf7f6e8999d483140fc42cb1
# Parent  7f0e49595f3104596035609f0e674a68a24c248b
Uploaded

diff -r 7f0e49595f31 -r 2ac71607aa60 SMART/Java/Python/CompareOverlappingSmallQuery.py
--- a/SMART/Java/Python/CompareOverlappingSmallQuery.py	Fri Jan 10 08:57:38 2014 -0500
+++ b/SMART/Java/Python/CompareOverlappingSmallQuery.py	Fri Jan 10 08:59:23 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()
diff -r 7f0e49595f31 -r 2ac71607aa60 SMART/Java/Python/CompareOverlappingSmallRef.py
--- a/SMART/Java/Python/CompareOverlappingSmallRef.py	Fri Jan 10 08:57:38 2014 -0500
+++ b/SMART/Java/Python/CompareOverlappingSmallRef.py	Fri Jan 10 08:59:23 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()