[Bioperl-l] Kmer counting

[Lee Katz]

Thanks Chris! I updated it so that bio seqio objects can be input also.
There is now a bioperl example too.

On Jun 21, 2017 23:50, "Fields, Christopher J" <cjfields at illinois.edu>
wrote:

> It’s probably best as a standalone library, particularly if it’s very
> focused on this specific need.  Saying that, I could see you adding code or
> a simple example script that would (as an example) read in sequences via
> Bioperl and perform kmer-based analyses on them.  Not that reading FASTQ
> via bioperl is very fast…
>
>
>
> chris
>
>
>
> *From: *Lee Katz <lskatz at gmail.com>
> *Date: *Wednesday, June 21, 2017 at 8:16 PM
> *To: *Chris Fields <cjfields at illinois.edu>
> *Cc: *"<bioperl-l at lists.open-bio.org>" <bioperl-l at mailman.open-bio.org>
> *Subject: *Re: [Bioperl-l] Kmer counting
>
>
>
> Yes this is what I mean but having looked at what I might need to change
> to make it bioperl-esque, I am thinking of just keeping it as standalone.
> I appreciate what you are offering but I think for now I will keep it as-is
> until I get a little more free time :)
>
>
>
> On Tue, Jun 20, 2017 at 10:47 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
>
> Hi Lee,
>
>
>
> Missed this email, apologies.  This primarily depends on how it would fit
> within Bioperl; since it’s primarily stand-alone and doesn’t require
> Bioperl, it probably doesn’t need to be in core.  We can certainly include
> it in the other Bio* distributions on the github page if needed (and add
> you to the repo as primary admin).  Is this what you mean?
>
>
>
> Thanks,
>
>
>
> chris
>
>
>
> *From: *Bioperl-l <bioperl-l-bounces+cjfields=il
> linois.edu at mailman.open-bio.org> on behalf of Lee Katz <lskatz at gmail.com>
> *Date: *Tuesday, June 6, 2017 at 12:17 PM
> *To: *"<bioperl-l at lists.open-bio.org>" <bioperl-l at mailman.open-bio.org>
> *Subject: *[Bioperl-l] Kmer counting
>
>
>
> 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.
>
>
>
>
>
> --
>
> Lee Katz
>
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