[Biopython-dev] Operations on kmers?

Alexey Morozov alexeymorozov1991 at gmail.com
Wed Feb 15 06:40:50 UTC 2017

Well, there is not much interest on mailing list, so I won't do it,
especially since my code now is pretty barebones. If anyone needs kmer lib,
kPAL appears to be the most powerful (as of now).

2017-02-07 10:11 GMT+08:00 Alexey Morozov <alexeymorozov1991 at gmail.com>:

> 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.

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