Bioperl: Bio::Tools::Blast->new on sequence file w/no hits, throws fatal exception. Any ideas?

[Tim Kunau (CBC)]

> 
> Throwing an exception guarantees that a blast object won't be used any
> further. It also provides a convenient screen, since you know that
> every object created will have at least one hit at or below your
> -signif cutoff.


I agree I should be trapping more thoroughly.

Regardless of the -signif value, there is important information I 
need about sequence results when no hits where found. I have no 
other method within BioPerl (by my knowledge) to determine 
$blastObj->matrix when Blast->new fails.

  
> If you are interested in every blast object, then omit the -signif
> parameter in your call to new() or parse(). I haven't come across a
> situation where I needed to work with Blast objects that had hits
> failing to meet my -signif criterion. I'd be interested to know if
> someone has. When working with files, you could just call new() a
> second time, omitting the -signif parameter. This wouldn't work when
> parsing from a stream.


In yeast this may be the case.

In the sequence data we're using, there are a number of hits below
our -signif threshold, as well as sequence files with no hit results 
at all. The files include the line:

          ***** No hits found ******

It would be useful to have a blast object without any hits as there
are other attributes of that object that are significant. Any ideas?

Thanks,

Tim
-- 
Timothy M. Kunau  kunau@ahc.umn.edu  Computational Biology Ctrs.
Genomic Database Administrator, Computing and Bioinformatics, AHC
612-626-6937  http://www.cbc.umn.edu/~kunau  http://www.cbc.umn.edu
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