[Bioperl-l] Taxa Id from blast report

[shalabh sharma]

Hey Peter,
       Thanks a lot, I really appreciate it. I wanted these things
implemented in blast from long time.

Thanks
Shalabh


On Thu, Apr 18, 2013 at 12:21 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> > On Thu, Apr 18, 2013 at 12:05 PM, Peter Cock <p.j.a.cock at googlemail.com>
> > wrote:
> >>
> >> 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
> >
> >
>
> On Thu, Apr 18, 2013 at 5:13 PM, shalu sharma <sharmashalu.bio at gmail.com>
> wrote:
> > Thanks a lot Peter.
> > Actually i still use legacy blast, so do i also get description of the
> hit
> > if i use tabular format and also do i have to format the database with
> some
> > modification ?
> > I really appreciate you help.
> >
> > Thanks
> > Shalu
>
> If you are using BLAST 2.2.28+ then you can also ask for the
> hit descriptions, also explored on my blog post. e.g.
>
> $ blastx -outfmt "6 std staxids stitle" ...
>
> or,
>
> $ blastx -outfmt "6 std staxids salltitles" ...
>
> Peter
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636