[Bioperl-l] Uniform syntax for Run objects
Mon, 15 Oct 2001 16:34:54 -0700
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?