Commit bdcb8913 by Pauline Pommeret

### [trx] sliding_pb

parent dfbd7258
 ... @@ -43,7 +43,7 @@ def pair_score(string, TRX): ... @@ -43,7 +43,7 @@ def pair_score(string, TRX): return TRX[max(potential)] return TRX[max(potential)] def match(sequence, TRX, shift): def match(sequence, TRX): """ """ Translates a raw ``sequence`` into a list of values of ``TRX``. Translates a raw ``sequence`` into a list of values of ``TRX``. ... @@ -63,5 +63,23 @@ def match(sequence, TRX, shift): ... @@ -63,5 +63,23 @@ def match(sequence, TRX, shift): return sequence_TRX 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.")
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!