[Biopython] Biopython local blastn query

[Peter Cock]

On Tue, Jul 30, 2013 at 6:02 PM, Ara Kooser <ghashsnaga at gmail.com> wrote:
> This will sound like a silly question. I found the nt.nal file that lists
> all the databses. How do I call the alias from biopython?
>
> I thought it would be something like this:
>
> nt = "/Users/arakooser/blast/db/nt.nal"
>
>  result = NcbiblastnCommandline(task="megablast",query="-", db=nt,
>                                    outfmt=5, perc_identity=100,
> out="temp.xml",
>                                    max_hsps_per_subject=1, num_alignments=1)
>
> But that throws an error letting me know that nothing was returned.
>
> ara

Just as a string in quotes, "nt",

NcbiblastnCommandline(task="megablast", query="-", db="nt", ...)

Peter