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Re: [BioPython] help with NCBIWWW.qblast Peter Fri Jan 02 16:00:19 2009

On Fri, Jan 2, 2009 at 7:50 PM, Jessica Grant <[EMAIL PROTECTED]> 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")

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