[Bioperl-l] parse EMBL Feature Table only
Dave Messina
David.Messina at sbc.su.se
Mon Dec 14 14:06:54 UTC 2009
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
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