[Bioperl-l] frac_aligned_query returning results >1.

Sendu Bala bix at sendu.me.uk
Fri Mar 2 06:23:45 EST 2007

Thiago Venancio wrote:
> Hi all,
> I have read a lot of threads regarding my issue, but still didn't get any
> efficient answer yet.
> I am with problems with frac_aligned_query(). It is returning  "> 1"
> results.
> I have just updated my SearhUtils.pm from:
> http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/Search/SearchUtils.pm

It shouldn't return results greater than 1. Please send me a minimal 
blast report that gives such results.

Make sure you only have one copy of SearchUtils.pm and that is the 
latest version (or that you are definitely using that latest version).

> The problem persists and, additionally, I get several warnings like:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Undefined sub-sequence (1507,1507) . Valid range = 1444 - 1507
> STACK: Error::throw

I don't know about that problem. See Chris's reply.

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