Chromosome Diagrams in Biopython
One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. I’ve just been updating the Biopython Tutorial (current version here, PDF) to include an example drawing this:
Here’s a PDF version too. This example just parses the Arabidopsis thaliana GenBank files to get the chromosome lengths and the tRNA gene placements. There are so many tRNA on the forward strand of Chr I that their labels are forced to overlap. Here the figure just uses a different color for each chromosome, but you can color each feature individually.
This kind of diagram is often used for showing the placement of SNPs or other loci of interest (e.g. disease or breeding markers).
P.S. Biopython produces these and other graphics using ReportLab, an open source Python library capable of outputting PDF, SVG, PNG, etc. Very handy.
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If anyone is interested, one reason for writing this enhancement was to produce the figures in this recently published open access manuscript, where we show the location of members of a resistance gene family on the potato chromosomes:
Jupe et al. (2012) http://dx.doi.org/10.1186/1471-2164-13-75
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