[BioPython] help with NCBIWWW.qblast

[Peter]

On Fri, Jan 2, 2009 at 7:50 PM, Jessica Grant <jgrant at email.smith.edu> wrote:
>
> Thanks for your response...actually I had failed to save my fasta file with
> unix line breaks.  This causes me so many problems and I guess over vacation
> I forgot that I need to deal with this.
>
> All is working now!
>
> Thanks!
>
> Jessica

That's interesting - but I'd be surprised if the NCBI can't cope with
mixed new lines in a qblast query (after all, their webserver will get
queries from Linux, Windows and Mac machines).

Was there a problem stemming from parsing the FASTA file?  How are you
reading in the FASTA file?  Have you tried opening the handle in
universal read lines mode?  e.g.

handle = open("example.fasta","rU")

Peter