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

[David Martin]

On Fri, 7 Sep 2001, Chervitz, Steve wrote:

>
> 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()?

Right.. that now works fine.

> 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...)

Maybe the perldoc should include a bold statement like
READ THE DOCUMENTATION FOR Bio::Parent::Object FOR DETAILS OF INHERITED
METHODS.

I'll print that out and stick it to my terminal ;-)

All working fine now. Many thanks.

..d

>
> Steve
>
>

----------------------------------
David Martin PhD
Bioinformatics Scientific Officer
Wellcome Trust Biocentre, Dundee
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