[Bioperl-l] Re: Bio::FPC

[Brian Osborne]

Jamie,

One of the challenges in Bioperl is creating a single coherent set of
modules from the many individual contributions. Could you tell us a bit
about your modules and how they overlap functionally with the existing
modules in Bio::Map? If you take a look at those modules you can see that a
good number of the more steadfast Bioperl authors have contributed to
Bio::Map, I'm sure that they'd like to see your modules integrate neatly
with the existing code.

I'm not one of these authors, I'm simply responding because it seems that
you'd like to get some discussion going.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jamie Hatfield
Sent: Monday, August 25, 2003 6:35 PM
To: BioPerl-List
Subject: Re: [Bioperl-l] Re: Bio::FPC

Again, how do I go about submitting this?

On Thu, 2003-08-14 at 09:34, Jamie Hatfield wrote:
> Yes, actually.  We are just now finishing up the fpc parser.  I was
> planning on soon asking the group how I would go about submitting it?
> It consists of 5 modules that we have put in the MapIO and Map
> namespaces.
> Bio::MapIO::fpc.pm
> Bio::Map::physical.pm
> Bio::Map::fpcmarker.pm  (sorry, but marker doesn't work)
> Bio::Map::clone.pm
> Bio::Map::contig.pm
>
> If you want to see how this object might be used, check out
> http://www.genome.arizona.edu/software/fpc/biofpc/index.html
>
> You'll see there documentation for the modules, and a few test cases or
> example usages.
>
> Also, we are trying to make a generic converter to let you load in a fpc
> file and generate the necessary GFF for GBrowse to display the fpc map.
> It's a quite simple display of the clones, markers, and contigs, but
> maybe that will be usefull as an alternative to WebFPC (a java view only
> version of fpc).  It works for us, but might not work for everybody.  We
> should be able to patch it up, though, if it's missing features.
>
> So, anyways, if somebody can let me know how to go about submitting it,
> we'll start the process.  I looked through the FAQ and it basically said
> to just post information if you have a module that you would like to
> contribute, so, here's the information.
>
> Jamie


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