[Biopython-dev] [Bug 1920] Bio.Geo does not support recent GEO files

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http://bugzilla.open-bio.org/show_bug.cgi?id=1920





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2005-12-24 06:39 -------
The current patch (patch 260) doesn't cope with current GPL files (GEO
platforms/annotation files) where the "before/after table comments" are
slightly different.

Also, the GEO Record object's __str__ method will attempt to show all the rows
in a data table, and for large GDS or GPL files this is a very bad idea -
python seems to lock up my computer as a result.

I propose to only print the first 20, then a ..., and the final record.  20 is
a reasonably low number and will not affect the existing test cases.

I have a revised patch prepared that tackles these two issues, but won't have
direct internet access until the New Year.  If anyone with CVS access feels the
urge, don't let this stop you from checking in the current patch and the
additional test cases.




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