[Biopython] Biopython local blastn query

[Ivan Gregoretti]

Sure there is a way to speed it up. Again, from BLAST's documentation:

 -num_threads <Integer, >=1>
   Number of threads (CPUs) to use in the BLAST search
   Default = `1'
    * Incompatible with:  remote


Ivan





Ivan Gregoretti, PhD
Bioinformatics




On Tue, Jul 30, 2013 at 1:44 PM, Ara Kooser <ghashsnaga at gmail.com> wrote:

> Here is what I did with everyone's suggestions that got things working:
>
>     result = NcbiblastnCommandline(task="megablast",query="-", db="nt",
>                                    outfmt=5, perc_identity=100,
> out="temp.xml",
>                                    max_target_seqs=1)
>
>
> The big thing I am noticing is that this is incredible slow. Currently I am
> blasting 4 databases with 6 query sequences.
>
> Is there a way to speed this up?
>
> I started a run a 11:38 and the first returned hit came across at 11:41. It
> looks like it's about 2-3 minutes per sequence.
>
> ara
>
>
> On Tue, Jul 30, 2013 at 11:08 AM, Peter Cock <p.j.a.cock at googlemail.com
> >wrote:
>
> > 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
> >
>
>
>
> --
> Quis hic locus, quae regio, quae mundi plaga. Ubi sum. Sub ortu solis an
> sub cardine glacialis ursae.
>
> Geoscience website: http://www.tattooedscience.org/
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>