[Bioperl-l] Bio::SeqIO::fasta.pm

[Lincoln Stein]

Matheiu should dig up the FASTA specification and tell us whether an empty 
name is optional.  If the FASTA spec doesn't deal with the case, then we must 
assume that the name is *not* optional.

Lincoln

On Friday 23 August 2002 01:07 pm, Hilmar Lapp wrote:
> Apparently not.
>
> Any votes from the core or from people on the list? I don't have a strong
> view here. I recall having seen somewhere that indeed the presence of the
> name is optional, but I'm not sure.
>
> One could argue for tolerant reader, strict writer ...
>
> 	-hilmar
>
> > -----Original Message-----
> > From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
> > Sent: Friday, August 23, 2002 9:27 AM
> > To: 'bioperl-l@bioperl.org'
> > Subject: FW: [Bioperl-l] Bio::SeqIO::fasta.pm
> >
> >
> > I was just testing something out, and it was accepting a
> > blank in the header.  If I actually wanted raw sequence, you
> > are correct of course.
> >
> > I found an old thread that made me think a > with a space or
> > nothing after it was valid, which was why I asked.  I hadn't
> > found anything recent, though I could have missed it.  The
> > thread never said what was the agreed upon standard?
> >
> > http://bioperl.org/pipermail/bioperl-guts-l/1999-November/001311.html
> >
> > Mathieu Wiepert
> > Medical Information Resources
> > Mayo Foundation
> > (507) 266-2317 Fax (507)-284-0360
> > wiepert.mathieu@mayo.edu
> >
> > > -----Original Message-----
> > > From: Hilmar Lapp [mailto:hlapp@gnf.org]
> > > Sent: Friday, August 23, 2002 11:23 AM
> > > To: Wiepert, Mathieu
> > > Cc: Bioperl
> > > Subject: RE: [Bioperl-l] Bio::SeqIO::fasta.pm
> > >
> > >
> > > Didn't someone post a FASTA definition document or link a
> > > while ago? AFAIK the ID is mandatory, you can't just have an
> > > empty line.
> > >
> > > Have you tried reading your seqs as format raw? Not sure
> > > whether that one strips all non-seq characters, and whether
> > > it can handle multiple seqs, but generally speaking 'raw'
> > > format is what you would do if you really don't care about
> > > anything except the sequence itself.
> > >
> > > 	-hilmar
> > >
> > > > -----Original Message-----
> > > > From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
> > > > Sent: Friday, August 23, 2002 7:50 AM
> > > > Cc: Bioperl
> > > > Subject: [Bioperl-l] Bio::SeqIO::fasta.pm
> > > >
> > > >
> > > > Hi,
> > > >
> > > > Is it valid to have a fasta file with no header info (other
> > > > than the >, with no spaces after).  I.e. something like
> > > >
> > > > ACACACACA
> > > >
> > > >
> > > > Would lead to blank primary_id, not sure what effect that
> > > > would have down the line.
> > > >
> > > > I ask because fasta.pm throws the "Can't parse fasta header"
> > > > error when there *is* a space after the >, but goes merrily
> > > > on if there is a \n.  And then dies later.  Just wasn't sure
> > > > what the expected agreed upon behavior is.
> > > >
> > > > I ran into this because I was testing a few sequence blasts,
> > > > and don't need a header really.  I figure it's not much use
> > > > to have a fasta file with a bunch of "empty" header lines,
> > > > but fasta only has a comment
> > > >
> > > > # FIX incase no space between > and name \AE
> > > >
> > > > So I wasn't sure what the intent is.
> > > >
> > > > -Mat
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> >
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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