[Bioperl-l] Blast parsing.

[Chervitz, Steve]

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

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
> ----------------------------------
> 
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