[Biopython] Support for k-mer analyses?

[Alexey Morozov]

As there is not so much interest in this task (and people in biopython-dev
were uncertain over whether it'd be useful to include kmer module into
Biopython distriution), I've decided not to make it. If anyone needs a
(non-Biopython) kmer library, there already are several. I haven't done a
proper comparison, but kPAL seems most developed.

2017-02-08 20:41 GMT+08:00 Alexey Morozov <alexeymorozov1991 at gmail.com>:

> Hi Alan, thanks for your feedback.
> You've thrown some ideas that haven't crossed my mind. I was just
> wondering: why did you even find it necessary to cache distributions? What
> was the scale of your work? In my experience, aminoacid distributions of
> six complete eukaryotic proteomes up to k of 6 or 7 could fit into
> something like seven or so gigs (with no optimisation, without even numpy),
> so I thought nucleotide distributions will be prohibitive in terms of RAM
> only when there are tens of them.
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170215/afe8e606/attachment.html>