Fwd: Re: Kmer counting

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Fwd: Re: Kmer counting

Roy Chaudhuri-3
Sorry, forgot to cc the list.

-------- Forwarded Message --------
Subject: Re: [Bioperl-l] Kmer counting
Date: Tue, 13 Jun 2017 14:01:00 +0100
From: Roy Chaudhuri <[hidden email]>
To: Lee Katz <[hidden email]>

Hi Lee,

Doesn't look like you got a reply so I'll chip in.

Your module certainly looks like it would be a useful addition to
BioPerl, but it would probably need some modification - an obvious one
would be to use Bio::Seq objects rather than reading the fastq files
directly, which would have the additional benefit of allowing you to
easily support all Bio::SeqIO file formats. You'd probably also need to
inherit from Bio::Root::Root. The jellyfish component might be best
separated out into bioperl-run.

There are some tips on contributing to BioPerl here:
http://bioperl.org/howtos/Advanced_BioPerl_HOWTO.html
http://bioperl.org/howtos/Best_Practices_HOWTO.html

There is some other kmer-counting code in the Scrapbook which you might
also take a look at:
http://bioperl.org/howtos/Scrapbook_HOWTO.html#item24

Of course, there are other non-BioPerl modules in the Bio:: namespace,
so it's fine to leave it as a standalone if you prefer.

Cheers,
Roy.

On 06/06/17 18:06, Lee Katz wrote:

> Hi, I was wondering if my module Bio::Kmer fits with bioperl. I put it
> onto cpan and have basic unit tests, but it doesn't inherit anything
> from bioperl.
>
>
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