prac4

bed.py

@@ -136,10 +136,14 @@ class BedEntry():
     def getInterval(self):
         return ival.Interval(self.chromStart, self.chromEnd)
 
-def dist(entry1, entry2):
+def dist(entry1, entry2, signed = False, centre2centre = False):
+    """ Calculate and return the BedEntry with the closest distance (from one end of the interval of this to the end of the interval of that).
+        If centre2centre is True, use the centre-to-centre distance instead.
+        If signed is True, the distance is negative if this interval is after the that.
+    """
     if isinstance(entry1, BedEntry) and isinstance(entry2, BedEntry):
         if (entry1.chrom == entry2.chrom):
-            return ival.dist(entry1.getInterval(), entry2.getInterval())
+            return ival.dist(entry1.getInterval(), entry2.getInterval(), signed, centre2centre)
     return None
 
 class BedFile:
@@ -282,6 +286,18 @@ class BedFile:
                 else: return None
         else: return None
 
+
+    def getOneOfClosest(self, item):
+        all = self.getClosest(item)
+        if all == None: return None
+        else: return next(iter(all))
+
+    def getOneOfOverlap(self, item):
+        all = self.getOverlap(item)
+        if all == None: return None
+        elif len(all) == 0: return None
+        else: return next(iter(all))
+
 def readBedFile(filename, format = 'Limited'):
     """ Read a BED file.
         format: specifies the format of the file,

ival.py

@@ -294,14 +294,31 @@ class Interval:
     def __sizeof__(self):
         return self.max - self.min
 
-    def dist(self, that):
-        if (self.min > that.max): return self.min - that.max # that interval is BEFORE this
-        if (self.max < that.min): return that.min - self.max # that interval is AFTER this
-        return 0
-
-def dist(first, second):
+    def dist(self, that, signed = False, centre2centre = False):
+        """ Calculate and return the closest distance (from one end of the interval of this to the end of the interval of that).
+            If centre2centre is True, use the centre-to-centre distance instead.
+            If signed is True, the distance is negative if this interval is after the that.
+        """
+        if not centre2centre:
+            if not signed:
+                if (self.min > that.max): return self.min - that.max # that interval is BEFORE this
+                if (self.max < that.min): return that.min - self.max # that interval is AFTER this
+            else: # distance is signed
+                if (self.min > that.max): return that.max - self.min # that interval is BEFORE this
+                if (self.max < that.min): return that.min - self.max # that interval is AFTER this
+            return 0
+        else:
+            thiscentre = (self.max - self.min) / 2 + self.min
+            thatcentre = (that.max - that.min) / 2 + that.min
+            return thatcentre - thiscentre if signed else abs(thatcentre - thiscentre)
+
+def dist(first, second, signed = False, centre2centre = False):
+    """ Calculate and return the closest distance (from one end of the interval to the other).
+        If centre2centre is True, use the centre-to-centre distance instead.
+        If signed is True, the distance is negative if the first is after the second.
+    """
     if isinstance(first, Interval) and isinstance(second, Interval):
-        return first.dist(second)
+        return first.dist(second, signed, centre2centre)
     return RuntimeError
 
 def union(first, second):
@@ -347,6 +364,10 @@ if __name__ == '__main__':
     k = Interval(24, 24)
     l = Interval(52, 55)
 
+    print('dist(b,a,signed=False,centre2centre=False)=', dist(b, a, signed = False, centre2centre=False))
+    print('dist(b,a,signed=True,centre2centre=False)=', dist(b, a, signed = True, centre2centre=False))
+    print('dist(b,a,signed=False,centre2centre=True)=', dist(b, a, signed = False, centre2centre=True))
+    print('dist(b,a,signed=True,centre2centre=True)=', dist(b, a, signed = True, centre2centre=True))
     t = IntervalTree()
     t.put(a, 'A')
     t.put(b, 'B')