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

[Brian Osborne]

Michael,

In Bio/Tools/Run/CAP3.pm you see this at the top:

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}++; }
}

If you add the letter y to @PARAMS does it work?


Brian O.

On May 6, 2009, at 10:39 AM, Michael Stubbington wrote:

> 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
>
>
>
>
>
> -----------------------------------------
> **************************************************************************
> The information contained in the EMail and any attachments is
> confidential and intended solely and for the attention and use of
> the named addressee(s). It may not be disclosed to any other person
> without the express authority of the HPA, or the intended
> recipient, or both. If you are not the intended recipient, you must
> not disclose, copy, distribute or retain this message or any part
> of it. This footnote also confirms that this EMail has been swept
> for computer viruses, but please re-sweep any attachments before
> opening or saving. HTTP://www.HPA.org.uk
> **************************************************************************
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l