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

[Hilmar Lapp]

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
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > > 
> > 
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