[Bioperl-l] parsing blast result: how to get query info?

[Jason Stajich]

% perldoc Bio::SearchIO

% perldoc Bio::Search::HSP::HSPI
% perldoc Bio::Search::HSP::GenericHSP

% perldoc Bio::Search::Hit::HitI
% perldoc Bio::Search::Hit::GenericHit

% perldoc Bio::Search::Result::ResultI
% perldoc Bio::Search::Result::GenericResult


On Tue, 4 Mar 2003, Jack Chen wrote:

> Hi James,
>
> Thank you for the reply and Jason for the informative page. I am
> wondering if the page is incorporated into some of the modules, so that it
> can be accessed using perldoc. Currently, there is no obvious way for me
> to know what methods are associated with a certain object.
>
> Jack
>
> -~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-
>  Jack Chen, Stein Laboratory
>  Cold Spring Harbor Laboratory
>  1 Bungtown Road
>  Cold Spring Harbor, NY, 11724
>  Tel: 1 516 367 8394
> -~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-
>
> On Tue, 4 Mar 2003, James Wasmuth wrote:
>
> > Check the HOWTOs, http://www.bioperl.org/HOWTOs/html/SearchIO.html
> >
> >
> >
> >
> >
> > Quoting Jack Chen <chenn at cshl.edu>:
> >
> > > Hi All,
> > >
> > > I have been unable to figure out how to retrive query sequence info.
> > > For
> > > example, when I use sequence A (in fasta format) to blast a database DB
> > > and get a blast file FH with a number of hits, how can I retrieve
> > > information for sequence A in my blast report, together with data for
> > > the
> > > hits? Sequence A could be one of a number of query sequences.
> > >
> > > Thanks,
> > >
> > > Jack
> > > -~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-
> > >  Jack Chen, Stein Laboratory
> > >  Cold Spring Harbor Laboratory
> > >  1 Bungtown Road
> > >  Cold Spring Harbor, NY, 11724
> > >  Tel: 1 516 367 8394
> > > -~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> >
> >
> >
> > --
> > Nematode Bioinformatics
> > Blaxter Nematode Genomics Group
> > Institute of Cell, Animal and Population Biology
> > Ashworth Labs
> > University of Edinburgh
> > King's Buildings
> > Edinburgh
> > EH9 3JT
> > UK
> >
> > 0131 650 7403
> >
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu