diff smart_toolShed/commons/core/coord/SlidingWindow.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/coord/SlidingWindow.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,73 @@
+class SlidingWindow(object):
+        
+    def __init__( self, length = 1, overlap = 1 ):        
+        self._length = length
+        self._overlap = overlap
+        self._start = 1
+        self._end = length
+        self._step = length - overlap
+
+    def slideWindowOnce(self):
+        self._start = self._start + self._step
+        self._end = self._end + self._step
+    
+    def getStart(self):
+        return self._start
+    
+    def getEnd(self):
+        return self._end
+    
+    def setStart(self, start):
+        self._start = start
+    
+    def setEnd(self, end):
+        self._end = end
+    
+    def getLength(self):
+        return self._length
+    
+    def getOverlap(self):
+        return self._overlap
+    
+    def setLength(self, length):
+        self._length = length
+        
+    def setOverlap(self, overlap):
+        self._overlap = overlap
+    
+    def getSlidingMsg(self):
+        return "Window is sliding : %s %s" %(self._start, self._end)
+
+class SlidingWindowToCountMatchingBases(SlidingWindow):
+    
+    def getSetLengthOnWindow( self, iSet ):
+        if self._isSetIncludedInTheWindow(iSet):
+            return iSet.getLength()
+        if self._isWindowIncludedInTheSet(iSet):
+            return self._length
+        elif self._isSetOverlapTheRightSideOfTheWindow(iSet):
+            return self._end - iSet.getMin()+1
+        elif self._isSetOverlapTheLeftSideOfTheWindow(iSet):
+            return iSet.getMax() - self._start+1
+        
+    def getCoordSetOnWindow( self, iSet ):
+        if self._isSetIncludedInTheWindow(iSet):
+            return iSet.getStart(), iSet.getEnd()
+        if self._isWindowIncludedInTheSet(iSet):
+            return self.getStart(), self.getEnd()
+        elif self._isSetOverlapTheRightSideOfTheWindow(iSet):
+            return iSet.getStart(), self.getEnd()
+        elif self._isSetOverlapTheLeftSideOfTheWindow(iSet):
+            return self.getStart(), iSet.getEnd()
+        
+    def _isSetIncludedInTheWindow(self, feature):
+        return feature.getMin() >= self._start and feature.getMax() <= self._end
+    
+    def _isWindowIncludedInTheSet(self, feature):
+        return self._start >= feature.getMin() and self._end <= feature.getMax()
+
+    def _isSetOverlapTheRightSideOfTheWindow(self, feature):
+        return feature.getMin() <= self._end and feature.getMin() >= self._start
+
+    def _isSetOverlapTheLeftSideOfTheWindow(self, feature):
+        return feature.getMax() <= self._end and feature.getMax() >= self._start