[Biopython-dev] [Bug 2671] New: Including GenomeDiagram in the main Biopython distribution

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2671

           Summary: Including GenomeDiagram in the main Biopython
                    distribution
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: lpritc at scri.sari.ac.uk


Thanks largely to the efforts of Robert Cadena, we have modified GenomeDiagram
so that it plays nicely with the current CVS of Biopython and would like to
propose its inclusion as part of the main distribution.

GenomeDiagram is described in a Bioinformatics publication
(http://dx.doi.org/10.1093/bioinformatics/btk021), and is useful for
construction of circular and linear  images of biological sequence data, with a
specific domain of visualisation of large-scale genomic, comparative genomic
and other data with reference to a single chromosome or other biological
sequence as publication-quality vector graphics.  It's based on the Reportlab
backend, and can be used to produce rastered and streamed image output, too.

The major changes that have been made to the version previously available at
http://bioinf.scri.ac.uk/lp are:

Class names have been changed and no longer have the GD prefix

References to 'colour' have been changed to 'color', but both spellings are
still permitted in function calls, for backwards-compatibility

The default font has been changed to 'Vera', which is shipped with Reportlab,
to avoid some problems with unavailable fonts

Code for wx widgets has been removed, although the Observer/Observable code
remains, allowing user widgets to hook into the code, if that's desirable.

Some test code is included, testing colour translation and the ability to
produce PDF output in circular and linear diagram formats.

Other minor changes to reduce deprecation warnings (those in Reportlab proper
remain, however), and to remove code that caused font issues.

There are known issues, still.  Writing to a raster format, such as PNG, uses
Reportlab's renderPM code, which defaults to using fonts that are not installed
by Reportlab itself, anymore.  This is a Reportlab issue and doesn't affect
production of PDF output, so testing currently only checks the ability to
generate PDF output.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.