[Bioperl-guts-l] [Bug 2075] rpsblast parse problem w/r frame and strand

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Thu Aug 24 09:54:24 EDT 2006


------- Comment #5 from bix at sendu.me.uk  2006-08-24 09:54 -------
(In reply to comment #4)
> I have made changes which catch the Frame for RPS-BLAST and pass it to the
> handler (based on debugging statements), but nothing changed via the script so
> they haven't been committed yet.  This is an odd error as strand() isn't
> determined by the BLAST report data but by the query/hit start and end
> positions (says so right in SearchIO::blast).

Like I say, the code deliberatly avoids setting the strand if RPSBLAST is
detected. (It will also have overrriden any Frame you supplied to it.) See
lines 220 and 221 of Bio::Search::HSP::GenericHSP.

That's why I suggest the fix might be easy; potentially just get rid of those
lines. It just needs someone to spend a little time investigating it properly
to make sure there's no subtle problem with making that change. Having never
done an RPSBLAST myself I don't want to just jump in there and make the change
thoughtlessly. If you're feeling brave however... 

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