[Bioperl-l] Taxa Id from blast report

[Peter Cock]

On Thu, Apr 18, 2013 at 4:17 PM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
> Hi All.
>           I have a default blastx report and i want to get taxa ids from it
> along with other usual information. I am using Bioperl to parse the blast
> report, but i don't know how to get taxa ids.
>
> Thanks
> Shalu

If you upgrade to the latest BLAST+ and you can have this as a
column in the tabular output - easy to parse in Perl etc:
http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html

For example,

$ blastx -outfmt "6 std staxids" ...

Peter