[Bioperl-l] StandAloneBlast->blastall array of Bio::Seq objects

Sendu Bala bix at sendu.me.uk
Thu Dec 14 09:10:43 EST 2006


Andrew Stewart wrote:
> I am trying to StandAloneBlast->blastall an array or Bio::Seq  
> objects.  The documentation claims that blastall can be passed a file  
> name,

You're referring to 'In addition, sequence input may be in the form of 
either a Bio::Seq object or or an array of Bio::Seq objects'? I agree 
its not clear, but supplying a reference to an array is still supplying 
an array. Anyway, I'll clarify it.


In any case, the usage for the method is what you should pay attention to:

> Usage:
> 	$seq_array_ref = \@seq_array;  # where @seq_array is an array of  
> Bio::Seq objects
> 	$blast_report = $factory->blastall(\@seq_array);
> 
> Should this be...
> $report = $factory->blastall(@seq_array);
> or
> $report = $factory->blastall(\@seq_array);
> ???

It should be exactly what it says. A reference to the array.


> And if you are blastall'ing an array of Seq objects, then does  
> blastall just return one big blast report or should I be expecting an  
> array of blast reports?

Returns : Reference to a Blast object or BPlite object
            containing the blast report.

That means, just one big object, not an array.


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