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recording for each position how many A/T/C/G (the key) you see from the input list in python?

I have a list of kmers. I want to make a function that take kmers with same lend (5) and generate a PFM. The list is like ["TTTTA","TTTGA"] . I mean, record how many A/T/C/G you see from the input list. So far , I have this: 

def make_pfm(sites, k=5):

pmf1= []

pfm = {"A":[1]*k, "T":[1]*k, "C":[1]*k, "G":[1]*k}

return pmf1

The output that I'm looking for is like:

{'A': [1, 1, 1, 1, 2], 'C': [1, 2, 1, 1, 1], 'T': [2, 1, 2, 1, 1], 'G': [1, 1, 1, 2, 1]}

I will appreciate very much any help. Thanks!

gene sequence alignment blast sequencing
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written by Kevin_Smith • Kevin_Smith

This sounds a lot like homework...

A = sum([x.count('A') for x in list_of_kmers])
C = sum([x.count('C') for x in list_of_kmers])
G = sum([x.count('G') for x in list_of_kmers])
T = sum([x.count('T') for x in list_of_kmers])

Also what is PFM? Im going to guess that my Google result of "Pelvic Floor Muscle" is not accurate.

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written by John John

I tried the code bellow, but the output don't make sense , I see : {'A': [1, 1, 1, 1, 1, 1, 1], 'C': [1, 1, 1, 1, 1, 1, 1], 'T': [1, 1, 1, 1, 1, 1, 1], 'G': [1, 1, 1, 1, 1, 1, 1], (6482, 4427, 4626, 6087): 'AGTCCG\n'} PFM is just for call the python dictionary , pelvic floor muscle lol.

What do you think that is wrong? Thanks!

def make_pfm(list_of_kmers, k=5):

pfm = {"A":[1]k, "T":[1]k, "C":[1]k, "G":[1]k}

for x in list_of_kmers:

A = sum([x.count('A') for x in list_of_kmers])

C = sum([x.count('C') for x in list_of_kmers])

G = sum([x.count('G') for x in list_of_kmers])

T = sum([x.count('T') for x in list_of_kmers])

pfm[A, C, G, T] = x

return pfm

print make_pfm(list_of_kmers, k=7)

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written by Kevin_Smith • Kevin_Smith

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