[Bioperl-l] Re: Bio::FPC

[Jamie Hatfield]

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


On Mon, 2003-08-11 at 16:21, Yee Man Chan wrote:
> Hi Jamie and all,
> 
> 	My boss asked me to parse an FPC file. So I searched the bioperl
> mailing list archive for "FPC". I found that there was a discussion back
> in Nov 2002 about it. I am wondering whether this FPC parse is done or
> not. If it is workable now, can anyone tell me where I can download it?
> Otherwise, can someone point me to a spec of an FPC parser?
> 
> Thanks a lot.
> Yee Man
> 
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