[Bioperl-l] frac_aligned_query returning results >1.

Thiago Venancio thiago.venancio at gmail.com
Fri Mar 2 11:14:20 EST 2007


Hi Sendu,

Great to know you fixed the problem.
I have updated the SearchUtils and seems to be correct now.

Best!

Thiago


On 3/2/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> 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!
>



-- 
"The way to get started is to quit talking and begin doing."
      Walt Disney

========================
Thiago Motta Venancio, MSc
PhD student in Bioinformatics
University of Sao Paulo
========================


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