Biopython How to generate random Position-Weight Matrices

Question

[romeasy]

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.

Answer 1

[romeasy]

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.

[mdsiddra]

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?