update

Author: Bill Majoros

FastbTrack.py

@@ -34,6 +34,7 @@
 #   bool=track.isContinuous()
 #   track.save(FILEHANDLE)
 #   array=track.getNonzeroRegions() # returns array of Interval
+#   array=track.getZeroRegions() # returns array of Interval
 #   bool=track.anyZeroValues() # only for continuous tracks
 #   array=track.getContiguousRegions() # returns an array of Interval with 
 #      "value" attribute added
@@ -97,19 +98,35 @@ def getContiguousRegions(self):
         intervals.append(interval)
         return intervals
 
-    def getNonzeroRegions(self):
+    def getZeroRegions(self):
         """getNonzeroRegions() returns array of Intervals"""
         data=self.data
         if(self.isDiscrete()): raise Exception("track is not continuous")
         L=len(data)
         intervals=[]
         begin=None
+        for i in range(L):
+            x=data[i]
+            if(x==0 and (i==0 or data[i-1]!=0)): begin=i
+            elif(x!=0 and i>0 and data[i-1]==0):
+                intervals.append(Interval(begin,i))
+        if(L>0 and data[L-1]==0):
+            intervals.append(Interval(begin,L))
+        return intervals
+
+    def getNonzeroRegions(self):
+        """getZeroRegions() returns array of Intervals"""
+        data=self.data
+        if(self.isDiscrete()): raise Exception("track is not continuous")
+        L=len(data)
+        intervals=[]
+        begin=None
         for i in range(0,L):
             x=data[i]
-            if(x>0 and (i==0 or data[i-1]==0)): begin=i
-            elif(x==0 and i>0 and data[i-1]>0):
+            if(x!=0 and (i==0 or data[i-1]==0)): begin=i
+            elif(x==0 and i>0 and data[i-1]!=0):
                 intervals.append(Interval(begin,i))
-        if(L>0 and data[L-1]>0):
+        if(L>0 and data[L-1]!=0):
             intervals.append(Interval(begin,L))
         return intervals
 

SumLogProbs.py

@@ -49,8 +49,8 @@ def sumLogProbs(x):
     return largestValue+math.log(sum)
 
 
-v=[math.log(0.0001),math.log(0.0002),math.log(0.0003)]
-print(math.exp(sumLogProbs2(math.log(0.1),math.log(0.2))))
-print(math.exp(sumLogProbs(v)))
+#v=[math.log(0.0001),math.log(0.0002),math.log(0.0003)]
+#print(math.exp(sumLogProbs2(math.log(0.1),math.log(0.2))))
+#print(math.exp(sumLogProbs(v)))
 
 

Transcript.py

@@ -218,7 +218,7 @@ def shiftCoords(self,delta):
         self.end+=delta
 
     def loadExonSequences(self,axisSequenceRef):
-        exons=self.exons
+        exons=self.getRawExons()
         numExons=len(exons)
         strand=self.strand
         for i in range(numExons):
@@ -236,7 +236,7 @@ def loadExonSequences(self,axisSequenceRef):
         return True
 
     def loadTranscriptSeq(self,exisSequenceRef):
-        exons=self.exons
+        exons=self.getRawExons()
         numExons=len(exons)
         firstExon=exons[0]
         self.loadExonSequences(axisSequenceRef)