[Bioperl-l] parsing blast reports

[Brian Osborne]

Martin,

Take a look at the SearchIO HOWTO,
http://bioperl.org/HOWTOs/html/SearchIO.html, it may help with some of your
SearchIO questions.

You're absolutely right about it being awkward to trace the location of
inherited methods, but this is intrinsic to Perl. The bptutorial.pl script
can help out here, take a look at this:

http://bioperl.org/Core/Latest/bptutorial.html#v.1_appendix:_finding_out_whi
ch_methods_are_used_by_which_bioperl_objects


Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Martin A. Hansen
Sent: Tuesday, September 30, 2003 7:58 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] parsing blast reports

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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