[Bioperl-l] Using Muscle parameter within bioperl

Sendu Bala bix at sendu.me.uk
Wed Dec 20 09:08:16 EST 2006

Shrinivasrao P. Mane wrote:
> Hi,
> I need to run muscle using bioperl. This is how I do it in command line.
> muscle -in inv.fasta -out inv.aln -log inv.log -verbose -quiet
> I used the following in perl script
> my $muscle = new Bio::Tools::Run::Alignment::Muscle(-format =>  
> 'clustalw',  -verbose=>'', -quiet=>'', -log='inv.log');
> The program runs and produces the result file but it doesn't create a  
> log file nor does it stop sending output to STDOUT (-quiet).
> Could anybody help me with this?

The Muscle arguments don't take dashed args. To make switches active you 
need to set them to some true value. So (-verbose => 1, quiet => 1, log 
=> 'inv.log'). Verbose may not do what you want since it is both a 
Bioperl option and a Muscle option; if you want the latter try using 
verbose => 1.

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