[Biopython] SeqIO.parse Question

[Peter]

On Mon, Nov 23, 2009 at 11:34 AM, João Rodrigues <anaryin at gmail.com> wrote:
> My definition of FASTA is actually what BLASTp requires. It's quite a picky
> tool :) I had already understood that FASTA is quite... lax. But I thought I
> was missing something, thus asking the list. Is the alphabet patch already
> included?

No, the strict alphabet checking in the Seq object is not merged (yet).
This is potentially a contentious issue, and may break existing scripts
which really on the current lax behaviour. I am wondering about making
this trigger a warning in the next release of Biopython as a step towards
making the strict check the default, but this needs further debate.

> Thanks for the tip on the leading white space, had missed that :)

Sure.

Peter