[trx] sliding_pb

trx.py

@@ -43,7 +43,7 @@ def pair_score(string, TRX):
         return TRX[max(potential)]
 
 
-def match(sequence, TRX, shift):
+def match(sequence, TRX):
     """
     Translates a raw ``sequence`` into a list of values of ``TRX``.
 
@@ -63,5 +63,23 @@ def match(sequence, TRX, shift):
     return sequence_TRX
 
 
+def sliding_pb(sequence_TRX, shift=72):
+    """
+    Uses ``sequence_TRX`` (dictionary where keys are position in sequence and
+    values are TRX values associated with the nucleotides) and computes the
+    mean value on ``shift`` (int) sliding bp.
+
+    Default ``shift=72``.
+
+    Returns a dictionary.
+    """
+    # Test if sequence_TRX and shift have compatible length
+    if len(sequence_TRX) > shift:
+        sliding_TRX = {}
+        for position in xrange(0, len(sequence)-shift):
+            sliding_TRX[position] = numpy.round(numpy.mean([sequence_TRX[i] for i in xrange(position, position+shift)]), decimals=2)
+        return sliding_TRX
+    elif:
+        raise ShiftOutOfRange("Choosen shift is too long for query sequence.")