[Bioperl-l] Uniform syntax for Run objects

[Peter Schattner]

I've noticed that the input format used with new object
Bio::Tools::Run::RemoteBlast is different from that of the other "Run"
objects  StandAloneBlast.pm , Clustalw.pm and Tcoffee.pm .

RemoteBlast  uses this format for setting up a 'factory':

my  $remote_blast = Bio::Tools::Run::RemoteBlast->new('-verbose' => $v,
            '-prog' => $prog,
            '-data' => $db,
            '-expect' => $e_val,
            );

In contrast,  StandAloneBlast.pm , Clustalw.pm and Tcoffee.pm all use this
format (where the significant difference is that the leading '-' is not
required (or even permitted)):

my  $factory = Bio::Tools::Run::StandAloneBlast->new('prog' => 'blastn',
'data' => $nt_database ,
       '_READMETHOD' => 'Blast', 'output' => 'blastreport.out');

I think that we should have a uniform input  syntax for these related
modules.  I would prefer staying with the syntax used in
StandAloneBlast.pm , Clustalw.pm and Tcoffee.pm  because

1.  People already have code out there which uses it. And
2.  It makes it a little easier to use perl's AUTOLOAD function to handle
all kinds of other parameters to be sent to the programs without our
having to know about them ahead of time ( a  feature that
StandAloneBlast.pm , Clustalw.pm and Tcoffee.pm  currently  implement).

What are other's thoughts on this topic?

Peter