[Bioperl-l] Re: Bio::FPC

Wed Aug 27 18:05:06 EDT 2003

Bio::Map::Marker is really more like our clones.  A clone has a range
that it exists in contig (or map).  But FPCMarkers don't have a position
in a map.  They "hit" a clone.  That is why I felt it was necessary to
create a new class.  I don't see how these two ideas overlap.

On Tue, 2003-08-26 at 10:02, Ewan Birney wrote:
> 
> 
> 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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