[Bioperl-l] Re: SeqIO::swiss.pm + "gsequence"

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Fri, 15 Sep 2000 14:40:07 +0100

Sorry that I didn't respond yet but I think the point of empty seqs is
valid, and I wanted to change the code to allow for this unless someone
vetoes. The problem still remains how to do IO for empty seqs (e.g. in
FASTA you cannot have just the ID line, followed by the ID line of the next
seq). So, IO probably remains forbidden for empty seqs unless someone comes
up with a sensible solution.


Kris Boulez <krbou@pgsgent.be>@bioperl.org on 15.09.2000 07:36:07

Sent by:  bioperl-l-admin@bioperl.org

To:   Lorenz Pollak <lorenz@ist.org>
cc:   Hilmar Lapp <hlapp@gmx.net>, Bioperl <bioperl-l@bioperl.org>
Subject:  Re: [Bioperl-l] Re: SeqIO::swiss.pm + "gsequence"

Quoting Lorenz Pollak (lorenz@ist.org):
[ .. ]
> (btw: the next thing i encountered was that it was not possible to have
> empty sequences, which is a bit a problem if you want to give the
> possibility of entering a complete new sequence instead of loading
> one. has this behavior changed in the meantime?)
I recently asked a question about a related issue (fasta.pm not reading
entries with empty sequence), but got no reply. So I'll rephrase my
question ?

What's the (general) philosophy in BioPerl about reading/writing entries
with an empty sequence ?

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