[Bioperl-l] Bio::Tools::Run::Cap3 - Parameters

Michael Stubbington Michael.Stubbington at hpa.org.uk
Wed May 6 10:39:27 EDT 2009

Dear all,


I am using the Bio::Tools::Run::Cap3 wrapper to the Cap3 assembly
program. I have some reads that will only assemble if cap3 is used with
the '-y 150' option. This is fine from the command line but I can't work
out how to pass this option to the Cap3 factory object in my script.


If I do the following


my $params =  "y 150" ;

my $cap3Factory = Bio::Tools::Run::Cap3->new($params);

my $assembly = $cap3Factory->run($file);


Then I get an exception as follows:


------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Unallowed parameter: y !

STACK: Error::throw

STACK: Bio::Root::Root::throw

STACK: Bio::Tools::Run::Cap3::AUTOLOAD

STACK: Bio::Tools::Run::Cap3::new

STACK: /Users/mike/perlScripts/QGenotype.pl:150


If I don't try to pass any parameters to Cap3 it runs fine but just
fails to assemble the reads that need the -y 150 flag.


I'd very much appreciate any help with this. I'm pretty new to bioperl,
hope I haven't missed anything obvious!


Thanks in advance,





Mike Stubbington

Novel and Dangerous Pathogens

Health Protection Agency

Centre for Emergency Preparedness and Response

Porton Down




Tel: +44 1980 619812


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