[Bioperl-l] Blast parsing.

[David Martin]

On Tue, 4 Sep 2001, Chervitz, Steve wrote:

> David,
>
> Bio::Tools::Blast does in fact have methods to get at the data you mention.
> The reason why they're not obvious is that they're inherited from
> Bio::Tools::SeqAnal, the superclass of Bio::Tools::Blast. So you can access
> these methods from a Bio::Tools::Blast object:
>
>  $blastObj->database
>  $blastObj->database_release
>  $blastObj->database_letters
>  $blastObj->database_seqs

OK.. I'm a bit new to the concept of inheritance in Perl OO programming..

Many thanks.

..d

(and thanks to those who suggested BPlite.. It would have been the way to
go if this had not been available.)

..d

>
> Note that to get this data, you'll need to include a -STATS => 1 parameter
> when you call the Bio::Tools::Blast::parse() function. By default, database
> stats (among other things at the bottom of a Blast report) are not parsed
> for efficiency reasons.
>
> To get the name, length, and description of the query sequence:
>
>  $blastObj->query
>  $blastObj->length
>  $blastObj->query_desc
>
> This issue highlights a limitation with the Perl documentation tools which
> don't automatically include superclass information. There's a note in the
> Bio::Tools::Blast pod docs to see the superclass for additional
> functionality, but this isn't optimal. (It's my hope that a future perldoc
> release will have the ability to automatically link in superclass docs.)
>
> Steve
>
> > -----Original Message-----
> > From: David Martin [mailto:dmartin@bioinformatics.msiwtb.dundee.ac.uk]
> > Sent: Monday, September 03, 2001 8:54 AM
> > To: bioperl-l@bioperl.org
> > Subject: [Bioperl-l] Blast parsing.
> >
> >
> >
> > I am in need of a Blast parser so have turned to Bioperl.
> >
> > Having worked out what I think it is doing there seem to be
> > some gaps int
> > he details it can report.
> >
> > The Bio::Tools::Blast object doesn't have any methods for
> > returning the
> > name of the databases, the database statistics (number of
> > seqs/bases), or
> > the query sequence details (name, length, type etc.)
> >
> > Are there any plans for these to be included or should I be
> > looking at a
> > different module that may be able to help?
> >
> > ..d
> >
> > ----------------------------------
> > David Martin PhD
> > Bioinformatics Scientific Officer
> > Wellcome Trust Biocentre, Dundee
> > ----------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>

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