[Biopython-dev] Operations on kmers?

[Alexey Morozov]

Okay, I've asked on the users mailing list. If there are people expressing
interest, I'll make it, otherwise there's no reason to.

2017-02-06 20:26 GMT+08:00 Peter Cock <p.j.a.cock at googlemail.com>:

> HI Alexey,
>
> On Fri, Feb 3, 2017 at 3:14 AM, Alexey Morozov
> <alexeymorozov1991 at gmail.com> wrote:
> > I've written a little library for k-mer based analyses, and eventually
> > decided to upload it to PyPI. Guess what? There are several modules for
> that
> > (https://pypi.python.org/pypi?%3Aaction=search&term=kmer&submit=search),
> > including my own (kmers).
>
> I have used khmer from Python http://khmer.readthedocs.io/en/v2.0/
> but have not looked into the more recent options.
>
> > Is there a chance one of those can make it to Biopython?
>
> Potentially, although it may not be a good fit.
>
> > It's usually better to have a singe universally available library
> > than a bunch of in compatiblble ones.
>
> Yes :)
>
> > I'm willing to work on it, probably in cooperation with folks that made
> > other packages, but I don't have a slightest idea whether it's gonna be
> > accepted to Biopython. k-mers are still somewhat obscure, after all. If
> it
> > is, where, in your opinion, does it belong? A separate Bio.Kmers module,
> > a submodule of Bio.Statistics or Bio.Cluster? Something else?
>
> If Biopython were to have some k-mer support, probably a separate
> top level module, Bio.kmers (lower case as per PEP8 unless
> constrained by historical choices, so not Bio.Kmers) would be best.
> Or, under Bio.SeqUtils might work too?
>
> My gut feeling is that a one or two person effort would struggle to
> match some of existing Python libraries focused on kmers,
> especially for performance. However, if there is interest from
> the Biopython community that would be great.
>
> Regards,
>
> Peter
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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