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

[Kevin Brown]

BEGIN {

    @PARAMS     = qw(a b c d e f g m n o p s u v x);
    $PROGRAMDIR = '/usr/local/bin';

    # Authorize attribute fields
    foreach my $attr (@PARAMS) { $OK_FIELD{$attr}++;

}

That is the list of params that Cap3 will accept in the BioPerl module.
I'm guessing if you add the y to that list that it might work. 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Michael Stubbington
> Sent: Wednesday, May 06, 2009 7:39 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Bio::Tools::Run::Cap3 - Parameters
> 
> 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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