[Bioperl-l] fasta format

[Hilmar Lapp]

> -----Original Message-----
> From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
[...]
> 
> >\s+(.*)
> is valid, as described by Bill Pearson.  Should have null ID, 
> then description.
> 

I'm concerned about making this change. It radically changes the behaviour of the parser, even if this interpretation is the correct one (Bill, could you clarify?)

The reason I'm concerned is that I have seen many people putting a space between '>' and the ID when the copy-and-paste sequences, believe it or not, and be it correct or not. My point is that every web-server written using bioperl will break after this change when users enter a space between ID and '>', whereas it handled the situation fine before.

Looking elsewhere, the EMBOSS seqret (and hence entire EMBOSS I guess) does ignore whitespace between '>' and ID and takes the first word as the ID.

So that makes my second concern: I don't want bioperl behave much different than other sequence analysis toolkits.

	-hilmar