[Biopython-dev] library to create gel image

Peter biopython at maubp.freeserve.co.uk
Thu Feb 26 18:51:07 UTC 2009

On Thu, Feb 26, 2009 at 3:12 PM, Jose Blanca <jblanca at btc.upv.es> wrote:
> Hi:
> I'm writting an application that reads ABIF files (Applied Biosystems files)
> and generates a gel image. I'm able to read the trace (chromatogram) data
> from the file and now I would like to plot it. I don't want to plot every
> trace as a 2d graphic like in:
> http://www.mun.ca/biology/scarr/ABI377_chromatogram.jpg
> But to create a 2D gel image using all traces like in:
> http://www.fieldmuseum.org/research_collections/pritzker_lab/pritzker/images/ecran.jpg
> Any suggestion on which python library could I use?

Do you want to recreate the hexagonal grid, or would a simplified
rectangular grid do?

Do you need to be able to control the size, colour and intensity of
the spots (in order to recreate the something close to the original).
Do you get quality control information for nasty cases (e.g.
non-circular dots, say a ring donut shape)?

If you need this kind of fine control it would be a lot of work but
you certainly could do this "by hand" using a number of python
packages - for example ReportLab would let you generate PDF, PS, SVG
or bitmap images from the same drawing object.  Other backends might
be equally suitable.

> Of course, if anybody is interested in the code that I already got I'm willing
> to share it.
> Best regards,

The code for reading the trace (chromatogram) data from ABIF files
(Applied Biosystems files) might make a nice a addition to the
Bio.Sequencing module.


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