[Bioperl-l] Using Muscle parameter within bioperl

Shrinivasrao P. Mane smane at vbi.vt.edu
Tue Dec 19 14:46:56 EST 2006


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?
Thanks
Mane


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