[Bioperl-l] Map modules and IO

[Jason Eric Stajich]

Chad -

We would really like to have your stuff in there.  SimpleMap and the MapI
might need a more thorough evaluation - I don't want to change the API on
you too much once you start using it so we should make sure the function
names look okay to you.  We also need to get the Marker Inteface up there
- it will inherit from MappableI and contain a list of PositionI's.
Wasn't quite ready to push this stuff to production but I think we can
start to work them towards your needs.

My philosophy is that we can should build parsers in the XXXIO flavor - ie
SeqIO for Seq and TreeIO for Trees and AlignIO for SimpleAlign's and
SearchIO for Bio::Search data - I would like to see Bio::MapIO::mapmaker
for things parsing map results and have a factory interface in
Bio::Factory::MapFactoryI which has methods next_map and write_map which
operate on/return MapI objects.  Bio::MapIO should implement this
MapFactoryI interface.  This is in the spirit of our current system and
makes sense to me, but I am happy to convinced otherwise if you think this
is too much overhead for writing something simple.  I just envision
writing a number of parsers for different map formats (i.e. >2).

You can see the object design ideas in the
bioperl-live/modules/maps_and_markers.dia (or as PDF off the Docs link on
bioperl mainpage)  My apologies for not writing a formal proposal with all
the objects - most of this has been just conversations between Heikki,
Lincoln and I, and some simplification of the LSR genomic maps proposal.

As for the visualization and PS/PDF - I would like to think about putting
anything that depends on external modules for GUI in a separate module
like bioperl-gui, but am willing to be swayed on this one.  Part of the
philosophy the CORE has taken wrt to bioperl modules is:
  * building vanilla perl modules in bioperl-live
  * putting db dependent stuff in bioperl-db
  * gui dependent stuff in bioperl-gui,
  * c-extensions in bioperl-ext....

If this seems to restrictive or annoying to you, please consider making an
alternative proposal.  This policy is outlined briefly in the
here:
http://bioperl.org/pipermail/bioperl-l/2001-July/006026.html

The grand plan is to finish the basic map objects and build the db
interface layer to the proposed map schema in bioperl-db.  Any and all who
want to jump in and make this happen are welcomed, my apologies for not
introducing the proposal more formally have been extremely sidetracked
from this project.

-jason

On Mon, 26 Nov 2001, Chad Matsalla wrote:

>
> Hi all,
>
> I am intrigued by the new Bio::Map stuff and I'd like to commit a little
> something that use it.
>
> If anybody here works with Mapmaker for creating linkage maps you know how
> crappy^h^hspecial the postscript-rendered drawings of those maps is.
>
> I have a module that takes a mapmaker output file and, according to
> parameters passed in its construction, draws a really nice map and
> provides a PDF and an EPS. Our staff then mangle the EPS or Postscript to
> get the final product.
>
> I would like to provide a module that reads in a Mapmaker file and creates
> a Bio::Map::SimpleMap. I'll then feed that Object into a MapMangler that I
> created.
>
> Where would I put this module that reads Mapmaker files? It really isn't
> complicated but might be of use for somebody. Specifically, a Bio::Map::??
> object might be of use to somebody working with Mapmaker output.
>
> Chad Matsalla
>
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu