[Biopython-dev] Genome Diagram Default Behavior

Zachary Charlop-Powers zcharlop at mail.rockefeller.edu
Wed Aug 1 00:37:27 UTC 2012

Hello Biopython,

I am writing about a small feature that I would like to see implemented
(and could possibly help to implement it: I haven't contributed before and
am not sure exactly how tough this will be).  When using Genome Diagram to
draw features you can specify which strand to put a feature on. If the
strand is positive it will go above the track in the positive-facing
direction and if negative it will go below the track in the negative facing
direction. (seehttp://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc200) . That's a
great behavior. However if you use  strand="None", Genome Diagram will draw
the features inline with the track and always in the positive direction.
For myself, and probably others, keeping the direction of the features is
immensely useful as you can often get a sense of operon structure in
prokaryote genomes just by looking at the genes. Of course the forward and
the minus strands can be drawn but condensing small sections of genes to a
single track saves space when making images.

So, would it be possible to change the default behavior of Genome Diagram
to draw features inline (strand="None"), but to preserve their orientation?

zach cp

More information about the Biopython-dev mailing list