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

[Hilmar Lapp]

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
>