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

Kris Boulez krbou@pgsgent.be
Fri, 15 Sep 2000 14:47:01 +0200

Quoting hilmar.lapp@pharma.Novartis.com (hilmar.lapp@pharma.Novartis.com):
> 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.

For FastA files I would expect them to be (and have already encountered

>1 description of nr 1
>2 description of empty sequence

>3 description for nr3

I would vote for an empty line where the sequence should be.