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