Where can I find a Python implementation of Clark's or EM algorithm?

Question

[alec_djinn]

I have a list of allelic frequencies estimated by RFLP. I am looking for a Python implementation of the Clark's algo or the EM algo I can use to determine the haplotype frequencies. Can anyone point me out to some good resource?

Answer 1

[IP]

This is the implementation I did when doing a course in my masters, of course, it can be wrong. It is done to estimate genotype frequencies. But I think that it could be helpful for you. If you want, I could provide you the files qualities.txt and bases.txt. They show the error rate and the bases.

[IP]

The identation of the code looks fine, but does anyone know a way to post the whole code?

[GenoMax]

Put your code on Github and include a link for the public Gist. Biostars understands the links and will reproduce the code inline.

[IP]

Done! thank you very much!

[alec_djinn]

It doesn't look like the Clark's or the EM algo. Can you please post the input files? In general, however, I don't need to check the reads and the bases of a sequence. I expect to input a list of allelic frequencies and to get the haplotype frequencies as output.

[IP]

sure, here you have a link to the files in gist
I am not an expert on the EM- algorithm, but I think that you could modify the script to do what you want. The part of the EM algorithm begins at line 51, with the initial guess. and then it performs the Expectation and maximization steps.

[alec_djinn]

Unfortunately, this is not what I am looking for.