[Bioperl-l] FeatureI GFF output is not GFF version 2 compatible?

Mark Wilkinson mwilkinson@gene.pbi.nrc.ca
Fri, 10 Nov 2000 09:28:10 -0600

Hilmar, Do you have a parser that works?  Just *thinking* about designing one
to deal with the output as it stands "gives me the shivers" (to quote my
favorite novel), but we are quite desperate to get one up and running
quickly.... my head was churning over the problem last night in my sleep and
the closest I could come up with was to split the attributes section on the
"=" character,  and the last word of the previous list element would be the
key and the all-but-last-word of the current list element would be the
value... but that's awfully ugly!!

It would be better, all round, if the output of FeatureI->gff_string adhered
to the stated standard, rather than us building multiple parsers for the
different flavours of GFF2...

Sanger folks... comments?  Would anyone object if I tweaked the code?


Hilmar Lapp wrote:

> So, it's probably these people that rely on it in their scripts who should
> comment.

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK