Jason Stajich | 19 Apr 21:38 2013
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Re: Taxa Id from blast report

Did you provide -parse_seqids in the header?  

Peter dealt with related things here:
http://blastedbio.blogspot.com/2012/10/my-ids-not-good-enough-for-ncbi-blast.html

Jason
On Apr 19, 2013, at 1:05 PM, shalu sharma <sharmashalu.bio <at> gmail.com> wrote:

> Hi,
>    Thanks everyone for you inputs.
>  <at> 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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Jason Stajich
jason.stajich <at> gmail.com
jason <at> bioperl.org

Gmane