[Biopython-dev] Python_MKT

[Juraj Bergman]

Dear all,
I'm resending my implementation of the McDonald-Kreitman test.
Link to the description of the module:https://www.dropbox.com/s/zgnz8xwlcsispzf/Python_MKT.pdf
Link to the code:https://www.dropbox.com/s/1z3opj4rbb0ms14/Python_MKT.py
I apologise for the initial mistake of sending attachments instead of links.
Kind regards,
Juraj Bergman
P.S. Regarding the multi_short_path() function - I realize that it is very, very repetitive butI have not (yet) managed to find a suitable loop construction that would replace the current code. The multi_short_path() function is by far the most complex function of the modulebecause its purpose is to find the codon network with the least amount of overall nucleotide substitutions and the least amount of non-synonymous nucleotide substitutions (given any combination of codons). Each codon is being represented as multiple lists of two integers (depending on the overall amount of codons being processed). The first integer specifies the amount of synonymous and the second specifies the amount of non-synonymous substitutions.For example, if 10 codons are being fitted in a network, then there are 10x10 = 100 combinations of codon-codon pathways, each represented with a two-integer list, and out of these 100 lists, the 'best' 10 have to be chosen to get the most optimal codon network (and the repetitiveness of thefunction mainly arises because of this process). This is, in short, a description of the function and I would appreciate any pointers that would help to make the code more succinct :)