[Bioperl-l] Bio::Graphics support for floating point positions

Nathan Haigh n.haigh at sheffield.ac.uk
Wed Sep 5 10:22:44 EDT 2007


Chris Fields wrote:
> You mean something like this?
>
> http://www.bioperl.org/wiki/HOWTO_Discussion:Graphics
>
> chris
>
> On Sep 5, 2007, at 4:42 AM, Albert Vilella wrote:
>
>   

Nice!

On a similar (well, related to Bio::Graphics) topic, I've written a
script that uses markers that have been mapped from a model organism to
linkage groups in related species in order to estimate the location of
"unknown" markers in those linkage groups.

I'm using the Bio::Map::* modules for much of this work and then I use
Bio::Graphics to display the linkage groups of the non-model organism
with the putative position of the "unknown" markers. However, I've had
to do a bit of fudging to get Bio::Graphics to draw this data. The
problems I encountered are described below. I also have an open bug:
http://bugzilla.open-bio.org/show_bug.cgi?id=2343

1) Linkage maps are measured in cM - which can and are likely to be
non-integer values. Bio::Graphics needs integer values, so I simply
scaled all my cM measurements prior to drawing by *1000. However, the
ruler now doesn't represent the "true scale" - can this be adjusted?

2) Some markers map to 0cM. However, Bio::Graphics requires positions
>0. To get round this I simply incremented these positions by 1
(post-scaling), so they display almost in the correct place.

Is it possible/likely/wise to support positions starting at zero and
float positions? Would such support simply be to internalise what I have
already done outside Bio::Graphics into the Bio::Graphics modules and
have it display the correctly scaled ruler?

Thoughts comments welcome.

Cheers,
Nath


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