[Bioperl-l] specifying options in StandAloneBlast.pm

[Jason Stajich]

I guess non-dashed parameters were Peter's preference when he wrote it
originally.

I think the inconsistency is annoying too but it seems to have been
adopted across the bioperl-run implementations now...

If someone wants to own this module - we would do well to support blastcl3
as a drop in replacement for blastall as well so people can use NCBI's
client rather than webbased remoteblasting (although I guess you can't
really queue up a bunch of queries with it).

A whole bunch more enhancements probably ought to go into it as well since
this is probably one of the most commonly used bioperl runnable - yet it
doesn't really have a maintainer.  Mat Wiepert had voluntered before, but
I may have scared him off it...

-jason
On Tue, 8 Jul 2003, Michael R Olson wrote:

> 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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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu