[Bioperl-l] Re: Bio::FPC

[Brian Osborne]

Jamie,

And a "marker" can be a genetic marker, yes? A la Bio::Map::Marker? If you
take a look at this module you'll see that its definition of marker allows
any marker to have different positions in different maps (contig "map",
genetic map, physical map). This seems to overlap with your notion of
marker.

Here's my first impression. There's a parser, MapIO::mapmaker for mapmaker,
mapmaker makes maps from segregation data, genetic data. Your fpc makes
physical maps, yet physical and genetic maps can be merged to create
"integrated maps". Your fpcmarker must be closely related to
Bio::Map::Marker, in fact it's not clear that there should be an fpcmarker.
I would think that a Marker object could be a reasonably rich one, and it
could be created by fpc or any other program, it really shouldn't matter
much how it's created (in fact, all this new PopGen code must be ordering
markers to make maps, I'd think). Perhaps you should be using some of the
existing code in Bio/Map? Your thoughts?

Brian O.

-----Original Message-----
From: Jamie Hatfield [mailto:jamie at genome.arizona.edu]
Sent: Tuesday, August 26, 2003 11:46 AM
To: Brian Osborne
Cc: BioPerl-List
Subject: RE: [Bioperl-l] Re: Bio::FPC

Yes, definitly, discussion is great!

We had a little bit of a discussion about this back in November 2002,
when I proposed the idea, and it was suggested by Heikki to try to fit
it into either Bio::Map or Bio::Assembly.  Maybe I picked the wrong
one?  How about this...  I will describe a little bit about what fpc is,
for those who don't know, and those who know Bio::Map and Bio::Assembly
will tell me if it fits in their design.  ok?

FPC stands for FingerPrinted Contigs.  Its main purpose is to assemble
clones into contiguous regions of overlaps, based on the fingerprint of
the clones.  These fingerprints can be from agarose (sp?) gels, or HICF,
or simulated, or whatever.  Maybe this is more like Assembly?

Anyway, you have the clones, and there are also markers that hit the
clones, and aid in assembling the clones into contigs.  These are the
main 3 classes.  Clones, Contigs, Markers.  Contigs contain Clones.
Markers hit Clones.  Clones are hit by markers.

Contigs 1--m Clones
Markers m--m Clones

Is that a sufficient description of FPC, or do we need more to make a
good decision?

Thanks for initiating the discussion, Brian.

Jamie

On Tue, 2003-08-26 at 05:28, Brian Osborne wrote:
> 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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