[Biopython-dev] Proposed addition to Standalone BLAST

[Jeffrey Chang]

> What do you think about generalizing this somehow to get the kind of
> functionality you are talking about? I'm not sure if there is a better 
> way to do it, and I don't know how much overhead is introduced by
> copying the handle. So I'm very open to suggestions on this...

Sure.  Having some code that would help to diagnose errors in BLAST
reports would be a very nice feature.  Certainly more user friendly than
having SyntaxError this or SyntaxError that.

We would have to build this on top of the current exceptions, though.  
It's still nice to have the SyntaxErrors under the hood, as an explanation
on why the parser is complaining in the first place.

How are you copying the handle?  If you read the contents of the handle as
a string (ummm, could be iffy parsing PSI-BLAST on RAM-starved machines,
but probably not a problem), and then wrapped a StringHandle around it,
there should be little overhead aside from the string containing the blast
results.

Jeff