[Bioperl-l] parsing blast reports

[Jason Stajich]

Query sequence orientation $hsp->query->strand
Hit sequence orientation   $hsp->hit->strand

On Tue, 30 Sep 2003, Martin A. Hansen wrote:

> hi
>
> using Bio::SearchIO to parse blastn reports, how does one find out if a hit is
> on the leading or the complement strand?
>
> and is it only I who have trouble with these sorts of simple questions? i tried
> using Class::Inspector to view and test all the methods in
> Bio::Search::Hit::GenericHit and Bio::Search::HSP::GenericHSP, but i see
> nothing relating to strand ( "Plus / Plus" or "Plus / Minus" as seen in the
> blast report).
>
> it is rather diffecult, as a bioperl beginner, to pin down the function you need
> in order to solve a fairly simple question. tracing the inherited objects from
> the documentation in order to locate a specific functionality is awkward. and
> tracing the functionality from the code alone is painful. so what does one do?
>
> martin
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu