[Bioperl-l] fasta format

[Wiepert, Mathieu]

> 
> 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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