On 12/05/2011 10:08 AM, Peter Cock wrote:
I use Biopython's GenomeDiagram for this sort of thing, which
internally uses a Python library called ReportLab which can
produce PDF, SVG, PNG, etc. Sadly I doubt that would be
suitable for EMBOSS which would really want a C library.
GenomeDiagram has the notion of tracks - which can be
useful for separating different types of features which would
otherwise overlap (e.g. gene/mRNA/CDS) and other tricks.
It also has some defaults about which feature qualifiers
to use as the feature name (e.g. gene, locustag).
The EMBOSS solution to tracks would probably use the Sequence Ontology
to define the tracks, and use features below some specified tag (or set
of tags) for each track.
We can apply the same tracks to showfeat (the text display of features)
Tracks also simplify the issues of colours for features.
lindna has code for rendering features withg scaling and avoiding
overlaps which we could also, I hope, reuse.
Maybe not for the next release (release date 15th January, but code
freeze before Christmas) but we can provide applications for testing by
anyone interested after the release.
regards,
Peter Rice
EMBOSS Team
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