[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/ 
Bio/Tools/Run/StandAloneBlast.html#POD5)
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);
???

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

--
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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