Bioperl: Bio::Tools::Blast->new on sequence file w/no hits,

[Steve Chervitz]

Tim Kunau (CBC) writes:
 > > 
 > > I will change the bioperl Blast object so that it does not throw an
 > > exception if there are no hits when using a -signif criterion. This
 > > will go into effect for the 0.051 release. If anyone has objections,
 > > speak up now.
 > > 
 > 
 > In sequence files with no hit results at all, regardless of any value
 > for -signif, the files include the line:
 > 
 > 
 >     ***** No hits found ******

The Blast parser currently checks for this string, but not finding it
does not always mean that the Blast object will have hits since not
all versions of Blast use this string. This is an example of the type
of problem that arises when parsing a flat file format not intended
for data exchange. For now, we can cope.

 > It would be useful to have a blast object without any hits as there
 > are other attributes of that object (and the related file) that 
 > are significant. Could this also be incorporated into the behavior? 
 > Specifically:
 > 
 > 
 >     $blastObj->matrix

The Blast object currently does support the retrieval of the matrix
used, as well as other statistical parameters. Quoting from the
Blast.pm documentation: 

  matrix 
 
       Usage     : $blast_object->matrix();
       Purpose   : Get the name of the scoring matrix used.
                 : This is extracted from the report.
       Argument  : n/a
       Returns   : string or undef if not defined

(which of couse requires a valid blast object, but we're working on
that ;).

SteveC

 > Please let me know if there is any other information I can provide.
 > 
 > 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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