Hi,
I am looking for a way to generate random Position-Weight Matrices (PWM) using Biopython.
I have to use Biopython for various reasons (fast motif finding for instance) but seem to be unable to create a Motif or PWM object by hand.
Is there any method to create PWMs from either numpy arrays or by specifying the 'counts' variable explicitly?
Thanks for any suggestions.
Okay, I already solved it myself.
For anyone interested, here is how I did it:
def createRandomMotif (motifLength, alphabet):
counts = {}
for letter in alphabet.letters:
counts[letter] = [random.randint(0,100) for x in xrange(motifLength)]
return mat.PositionWeightMatrix(alphabet, counts)
x = createRandomMotif(6, alphabet)
print x
Console:
0 1 2 3 4 5
A: 0.20 0.22 0.12 0.31 0.27 0.23
C: 0.03 0.33 0.34 0.28 0.39 0.38
G: 0.33 0.00 0.24 0.26 0.02 0.23
T: 0.44 0.45 0.29 0.16 0.32 0.16
This generates a random motif matrix for any given alphabet and motif length (k-mer length) k.
I am also using biopython and I am looking for a way to generate 'WAG' matrix from aligned protein sequence file. What kind of matrix is this one? How does the formula is applied to calculate frequencies of amino acids?
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