[Bioperl-l] parse EMBL Feature Table only

Frank Schwach fs5 at sanger.ac.uk
Tue Dec 15 05:38:40 EST 2009

Thanks Dave,
good to know that I haven't overlooked something bleedingly obvious in
Bioperl that already does this :-)
No problem, I have already implemented a simple parser to do it, which
works fine for my files. 

On Mon, 2009-12-14 at 15:06 +0100, Dave Messina wrote:
> 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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