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

Nathan S. Haigh n.haigh at sheffield.ac.uk
Wed Sep 5 17:18:17 EDT 2007


Chris Fields wrote:
> On Sep 5, 2007, at 9:22 AM, Nathan Haigh wrote:
>
>> ...
>> 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
>
> There is this section in the GBrowse configure doc, which to me
> suggests there is a way to do what you want in Bioperl; you may have
> to delve into the Bio::Graphics or GBrowse code to work it out,
> though.  I think the GBrowse mail list archives also have more on this.
>
> chris
>
> .....
>
> F. DISPLAYING GENETIC AND RH MAPS
>
> GBrowse can be tweaked to make it more suitable for displaying genetic
> and radiation hybrid maps.
>
> The main issue is that the Bio::DB::GFF database expects coordinates
> to be positive integers, not fractions, but genetic and RH maps use
> floating point numbers.  Working around this is a bit of an ugly hack.
> Before loading your data you must multiply all your coordinates by a
> constant power of 10 in order to convert them into integers.  For
> example, if a genetic map uses Morgan units ranging from 0 to 1.80,
> you would multiple by 100 to create a map in ranging from 0 to 180.
>
> Create a GFF file containing the markers in modified coordinates and
> load it as usual.  Now you must tell GBrowse to reverse these changes.
> Enter the following options into the [GENERAL] section of the
> configuration file:
>
>  units = M
>  unit_divider = 100
>
> These two options tell GBrowse to use "M" (Morgan) units, and to
> divide all coordinates by 100.  GBrowse will automatically display the
> scale using the most appropriate units, so the displayed map will
> typically be drawn using cM units.
>


Thanks for for the pointer Chris!

>From what you've said, it appears they might have done a similar hack to
me - which is always nice to know! It seems then to me, that it may be
worth making the Bio::Graphic::* modules slightly more generic and
applicable for these situations. It's late, so does anyone have
suggestions before I start digging through Bio::Graphic::* modules in
the morning? Maybe you guys across the water have something to say by
the time I wake up in the morning!?

Thanks
Nath


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