[Bioperl-l] Bio::Tools::Run::Cap3 - Parameters
Michael Stubbington
Michael.Stubbington at hpa.org.uk
Wed May 6 14:39:27 UTC 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
/Users/mike/lib/perl5/site_perl/5.8.9/Bio/Root/Root.pm:357
STACK: Bio::Tools::Run::Cap3::AUTOLOAD
/Users/mike/lib/perl5/site_perl/5.8.9/Bio/Tools/Run/Cap3.pm:116
STACK: Bio::Tools::Run::Cap3::new
/Users/mike/lib/perl5/site_perl/5.8.9/Bio/Tools/Run/Cap3.pm:101
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
------------------------------------------------------------------------
----
Mike Stubbington
Novel and Dangerous Pathogens
Health Protection Agency
Centre for Emergency Preparedness and Response
Porton Down
Salisbury
SP4 0JG
Tel: +44 1980 619812
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