[BioPython] Tweaking GenomeDiagram
Peter (BioPython List)
biopython at maubp.freeserve.co.uk
Fri Mar 24 14:56:14 UTC 2006
This email is mainly aimed at Leighton Pritchard (who I have spotted
posting on the list in the past) as it concerns his (bio)python add-on,
GenomeDiagram:
http://bioinf.scri.ac.uk/lp/programs.html#genomediagram
First Query
-----------
I would like to attach labels to (selected) features.
For example, I am drawing a circular genome diagram with a selection of
colour coded genes - some of which I would like to have individually
labelled. This might be done in a similar way to the genome size tick
captions (i.e. horizontal text) or perhaps rotated text (radially aligned).
However, as far as I can tell from the documentation and the source
code, this is not built in.
Second Query
-------------
When drawing circular genomes following the examples, the major tick
marks seem to be at 1, 10001, 20001, ... (depending on the tick interval
size).
It would look much better to display 10000 rather than 10001 (or even,
leading to my third question, 10 Kb).
Third Query
-----------
I would like to have genome size "tick labels" in terms of kilo-bases or
mega-bases (i.e. 3 Kb rather than 3000, or 2 Mb rather than 2000000). I
have done this myself by "hacking the source code" but my implementation
is rather special case.
So, has anyone tried to tackle these issues before?
Thanks
Peter
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