[Bioperl-l] problems with 0.71 Bio::Tools::Blast

[Chervitz, Steve]

David Martin writes (Friday, September 07, 2001 9:15 AM):

> I have been using the Blast parser with a degree of success. 
> Thanks guys.
>
> One problem is that the documented methods in SeqAnal for 
> database_letters
> and database_seqs do not appear to be working.

Did you remember to include a -stats => 1 argument in your call to parse()?
Otherwise, it could be that the parser can't make sense of the parameters
section of the report due to a formatting change. This section of the report
is notorious for varying from one version of Blast to the next. What version
of Blast are you using?

> Also Bio::Tools::Blast::Sbjct doesn't ahve an accessor method to the
> Subject name, I am forced to access the data member directly (as
> ${$hit}{'_name'}).

Again, it's an inheritance issue. The Sbjct object inherits a name() method
from its Bio::Root::Object superclass. So none of this direct data member
access now. (We've just got to get a module documentation tool that can deal
with inheritance hierarchies...)

Steve