[Bioperl-l] parse EMBL Feature Table only

Dave Messina David.Messina at sbc.su.se
Mon Dec 14 09:06:54 EST 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:

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.


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:


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