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

[Wiepert, Mathieu]

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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