[Bioperl-l] Re: SeqIO::swiss.pm + "gsequence"
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
Kris Boulez <firstname.lastname@example.org> on 15.09.2000 13:47:01
To: HILMAR LAPP/PH/Novartis@PH
cc: email@example.com, Lorenz Pollak <firstname.lastname@example.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.