[Bioperl-l] parse EMBL Feature Table only

[Dave Messina]

Hi Frank,

You will need to look at the feature table parsing code that Bio::SeqIO::embl itself uses to read those lines, probably the _read_FTHelper_EMBL method:
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqIO/embl.html#POD12

Since you're trying to parse what is effectively a part of an EMBL record, and a somewhat complicated part at that, as you might imagine this could be a little hairy.

It might be easier to go the route you started down: add a fake header and a (relatively long) fake sequence, and go through Bio::SeqIO in the normal way.


Dave


PS — I suspect you may already be familiar with it, but for an overview on how to get at data in feature tables, look at the Feature Annotation HOWTO:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation