[Bioperl-l] problems with Bio::Tools::GFF

[Scott Cain]

Hi Jason and Lincoln,

I have a few concerns with Bio::Tools::GFF. The first is with the method
_from_gff3_string, which does a split on \t to separate columns.  I
think the GFF3 spec says it can be space delimited, so that should
probably be \s+.  Additionally, to split the groups column, it uses
\s*;\s*, but I think that spaces have to be escaped, therefore, it
should only split on ; and spaces would indicate a problem (especially
if one splits on spaces as indicated above).

Finally, it doesn't provide a method of accessing the sequence that is
optionally at the bottom of the file.  I am not exactly sure how to
implement that (or I would), but I suspect it will have to be handled in
the next_feature method.  Of course, the problem with handling it there
is that it is not a feature.

Scott

-- 
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Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory