[Bioperl-l] Taxa Id from blast report

[shalu sharma]

Hi,
    Thanks everyone for you inputs.
@Peter:
I got really excited when i saw that you can even get super kingdom, but
when i tried to test it i just got taxa ids but not the super kingdom. Do
you have any idea whats going wrong?
my command:
blastx  -query test.fas -db /db/ncbiblast/refseq/latest/refseq_protein
-max_target_seqs 1 -outfmt "6 staxids sskingdoms"

output:
246200    N/A
246200    N/A

Thanks
Shalu


On Thu, Apr 18, 2013 at 3:52 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> I agree they have finally listened and added features requested by users
> but I've been suggesting they have a compressed output format available
> from eutils or genbank for years but have made no headway ;- (
> What's so hard about gzip'ping the output? I'm sure it would go a long way
> toward solving all the problems we get with truncated replies from queries!!
>
> --Russell
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:
> bioperl-l-bounces at lists.open-bio.org] On Behalf Of Fields, Christopher J
> Sent: Friday, 19 April 2013 6:26 a.m.
> To: Peter Cock
> Cc: bioperl-l at lists.open-bio.org; shalu sharma; shalabh sharma
> Subject: Re: [Bioperl-l] Taxa Id from blast report
>
> On Apr 18, 2013, at 11:48 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
> > On Thu, Apr 18, 2013 at 5:32 PM, shalabh sharma
> > <shalabh.sharma7 at gmail.com> wrote:
> >> Hey Peter,
> >>       Thanks a lot, I really appreciate it. I wanted these things
> >> implemented in blast from long time.
> >>
> >> Thanks
> >> Shalabh
> >
> > Me too. You can get the descriptions from the plain text BLAST or XML
> > output already of course, but they're not so nice to work with.
> >
> > Peter
>
> NCBI has been much more receptive of user input over the last several
> years, much more so than in the past.  I understand the reasoning for
> dropping BLAST support (though there were definitely needless bumps in that
> process).
>
> chris
>
>
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