[Bioperl-l] fasta format

[Lincoln Stein]

I apologize for the previous message; I didn't see Bill's response before I 
sent it.

As I understand it, FASTA does makes a distinction between the ID and the 
description (Bill, please confirm). The regular expression to match the two 
is:

	/^>(\S+)\s+(.*)$/

So, given that Bill has confirmed that empty IDs are valid, if there is a 
space after the ">", then what comes afterward should be interpreted as the 
description, not the ID.

Lincoln

On Friday 23 August 2002 05:38 pm, Wiepert, Mathieu wrote:
> > I have seen many people use the perfectly acceptable
> >
> > 	>    [blanks] description 1
> >
> > 	asdf
> >
> > 	>    description2
> >
> > 	qwerty
>
> Thanks for he explanation, that sounds very reasonable, and I think is what
> should be implemented.  If there is a space, I would not expect the first
> word of the description to become my id.  For instance, given a header like
> this
>
> >   Hi I am the header description
>
> asdf
>
> bioperl makes 'Hi' the id.  This is because
>
> my ($id,$fulldesc) = $top =~ /^\s*(\S+)\s*(.*)/
>
> parses "   Hi I am the header description" that way.  I would not expect
> that behavior.
>
> If anyone can recall why this might be, let me know.  I saw some threads on
> what to do with a blank sequence, nothing with a blank header, or a header
> missing an id.  If people like it the way it is, I can put a comment in the
> code to that effect.  However, I would hate not to touch it just because
> people can't remember why it is the way it is.
>
> I'll mess around and execute the test scripts, see if those break with any
> of the changes I was testing.
>
> -Mat
>
> > Bill Pearson
> >
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>
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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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