[Bioperl-l] Re: Bio::FPC

Tue Aug 26 13:02:11 EDT 2003

On Tue, 26 Aug 2003, Brian Osborne wrote:

> 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 - I doubt the pop gen stuff will overlap at all with this stuff. but
the marker comment is right, though I can well believe there needs to be
specific FPC hooks for markers used for FPC stuff....

> 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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> >
> >
>
>
>
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