[Bioperl-l] GFF handling in SeqFeatureI

Mark Wilkinson mwilkinson@gene.pbi.nrc.ca
Tue, 20 Feb 2001 15:53:06 -0600


Since Matthews message earlier today I've been playing off and on all
day today trying to "break" the gff2 input/output with no success...

Can anyone send me an example GFF string to import, or a feature
definition to export, which will cause this error?  I checked the
GFF.t script and it seemed to work fine... or?  Which script were you
referring to Matthew?

Actually, there *is* a way to break it, but the thought of trying to
bullet-proof against that bug gives me the shivers!  If you have a
free-text value to a tag, and this free-text contains a semicolon, then
the attributes parser will read that semicolon as the delimiter for the
next set of tag/values... ugh!  Hopefully people wont use semicolons in
their freetext very often...


Hilmar Lapp wrote:

> Today saw an excellent (well, that's my personal view :)
> coproduction of 3 people:
> --
> ---
> Dr. Mark Wilkinson
> Bioinformatics Group
> National Research Council of Canada
> Plant Biotechnology Institute
> 110 Gymnasium Place
> Saskatoon, SK
> Canada