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

Andrew Stewart stewarta at nmrc.navy.mil
Wed Dec 13 20:06:14 EST 2006

I am trying to StandAloneBlast->blastall an array or Bio::Seq  
objects.  The documentation claims that blastall can be passed a file  
name, a Bio::Seq object, or an array of Bio::Seq objects, while the  
usage suggests that a reference to an array of Bio::Seq objects is  
what must be passed to blastall.

(from http://doc.bioperl.org/releases/bioperl-current/bioperl-live/ 
	$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);

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?

I've tried $report = $factory->blastall(@seq_array); which seems to  
work ok, except that when I process the results, there are only  
results for the first Seq object in the array.


Andrew Stewart
Research Assistant, Genomics Team
Navy Medical Research Center (NMRC)
Biological Defense Research Directorate (BDRD)
BDRD Annex
12300 Washington Avenue, 2nd Floor
Rockville, MD 20852

email: stewarta at nmrc.navy.mil
phone: 301-231-6700 Ext 270

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