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

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Fri, 15 Sep 2000 14:55:44 +0100

Hmm. What do others think / have encountered?

Could you volunteer to perform a couple of tests for various programs
reading FastA format files to see what they do upon the empty seq and
whether they choke? I'm not sure whether it's a good idea to produce files
that look sensible but make other programs choke because they violate
format specs.


Kris Boulez <krbou@pgsgent.be> on 15.09.2000 13:47:01

To:   HILMAR LAPP/PH/Novartis@PH
cc:   bioperl-l@bioperl.org, Lorenz Pollak <lorenz@ist.org>
Subject:  Re: [Bioperl-l] Re: SeqIO::swiss.pm + "gsequence"

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
> seq). So, IO probably remains forbidden for empty seqs unless someone
> 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.