[Biopython-dev] library to create gel image

[Jose Blanca]

Hi:
I've fishished a first version of a program that reads a list of Applied 
Biosystems fsa files and draws a virtual gel. It does not reads the sequence 
because my users are interested in fragment analysis, but the basic 
infraestructure is in place to do it.
It does what my users need. It's quite slow though, but I'm not investing time 
in optimizing it.
If anybody wants to take a look at the code is in:
http://bioinf.comav.upv.es/svn/gelify/gelifyfsa/
I distribute it under the GPL licence.
If you think that any part of the code could be of any use for the Biopython 
project I would be very please to give it to the comunity.
Best regards,

Jose Blanca

On Friday 27 February 2009 11:57:49 Jose Blanca wrote:
> On Friday 27 February 2009 11:45:59 Peter wrote:
> > On Fri, Feb 27, 2009 at 9:05 AM, Jose Blanca <jblanca at btc.upv.es> wrote:
> > That's much clearer - is the Genographer software showing the actual
> > image (zoomed as required, with the colours adjusted as required), or
> > an artificial recreation?
>
> Is an artificial recreation, the same as I'm trying to accomplish. I just
> want more resolution an automated process (genographer is a GUI
> application)
>
> > Are you trying to create this figure for illustrative purposes only?
> > I mean would a slightly cartoon like recreation be fine, or are you
> > trying to make it as realistic as possible?
>
> I want to analyze it.
>
> > I see you are having to reverse engineer their file format.  I guess
> > other people have tried this in the past so there may be more clues
> > out on the internet.  Have you tried emailing the company to see if
> > they would publish the file format specifications (unlikely I fear,
> > but worth asking).
>
> Fortunately the ABIF was reverse enginered by people more clever than me.
> And a couple of years ago Applied published an specification.
> http://bioinf.comav.upv.es/svn/gelify/gelifyfsa/src/doc/ABIF_File_Format.pd
>f You can't beleive everything in that specification, but it is a good
> start. Reading an abif file is not a problem, drawing the gel with as
> little coding as possible is another thing.
> Regards,
>
> Jose Blanca
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-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)