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

Michael Stubbington Michael.Stubbington at hpa.org.uk
Wed May 6 11:27:39 EDT 2009

Hi Brian,

Thanks for your reply.


If I do that it doesn't throw the exception any more but it also doesn't
successfully assemble the reads that need the -y 150 flag.





From: Brian Osborne [mailto:bosborne11 at verizon.net] 
Sent: 06 May 2009 16:09
To: Michael Stubbington
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Bio::Tools::Run::Cap3 - Parameters




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



    @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

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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