[Bioperl-l] frac_aligned_query returning results >1.

Sendu Bala bix at sendu.me.uk
Fri Mar 2 11:05:16 EST 2007

Thiago Venancio wrote:
> Hi Sendu and Chris,
> Thanks for the help.
> As I mentioned, I have updated my SearchUtils file from:
> http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/Search/SearchUtils.pm 
> <http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/Search/SearchUtils.pm>
> I am also using the lates BioPerl version, installed from CPAN.
> Please find a buggy blast report attached.
> In this case, the frac_aligned_query() outputs "1.04", but I have others 
> with " 1.57" for example.
> Just for a quantitative aspect, I got ">1" values in only 61 / 53,377.

Many thanks for that.

I've committed another fix for SearchUtils so please get revision 1.23 
and try again. Hopefully all 61 will no longer be >1, but if any are 
please send me sample blast files again.

For anyone interested, the bug was due to a completely unbelievable 
oversight on my part in the contig merging algorithm: I forgot to deal 
with contigs that were fully contained by others. Wow!

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