[Bioperl-l] specifying options in StandAloneBlast.pm

[Michael R Olson]

Is there any particular reason why StandAloneBlast.pm forces you to
enter parameters to blastall in this format:

my @params = ( 'p' => 'tblastn', 'd' => 'test.fa' );
my $factory = new Bio::Tools::Run::StandAloneBlast(@params);

My problem with this is that arguments tend to get specified as -p, -d,
etc.  If you say:

my @params = ('-p' => 'tblastn', '-d' => 'test.fa' );
my $factory = new Bio::Tools::Run::StandAloneBlast(@params);
$factory->blastall(\@seqs);

It complains that - is an invalid option.  It's not a huge issue, but it
seems fairly counterintuitive to me that including the hyphen is
illegal, especially when calling blastall from the command line would
require it.  Is there some kind of logic behind this?  If not, should I
send it to bugzilla as an enhancement request, or buck it up and rewrite
my code?
Thanks
Mike

---------------------------
Mike Olson
St. Olaf Mycobacterium Lab
St. Olaf College
Northfield, MN
507-646-3102
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