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

[Michael Stubbington]

Jonathan,

 

Thanks a lot for this advice. It now all works for me. 

 

Strangely my cap3 installation is not in /usr/local/bin but everything
works fine without me having to change $PROGRAMDIR in cap3.pm

 

Thanks to everyone else involved in this thread for their efforts in
improving Bio::Tools::Run::Cap3.

 

Best wishes,

 

Mike

 

________________________________

From: Jonathan Crabtree [mailto:jonathancrabtree at gmail.com] 
Sent: 06 May 2009 16:46
To: Kevin Brown
Cc: Michael Stubbington; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Bio::Tools::Run::Cap3 - Parameters

 


The "new" argument to Cap3 expects an array, not a string.  So I think
you need to do this:

my $cap3Factory = Bio::Tools::Run::Cap3->new('y',  '150');

rather than this:

my $cap3Factory = Bio::Tools::Run::Cap3->new('y 150');

Otherwise it will silently ignore the parameter.  There are also several
problems with the Cap3 module itself, at least the version shown here:

http://cpansearch.perl.org/src/CJFIELDS/BioPerl-run-1.6.1/Bio/Tools/Run/
Cap3.pm

Those problems are:

1. "y" is not in the PARAMS array, as Brian and Kevin have noted
2. $PROGRAMDIR appears to be hard-coded to /usr/local/bin (OK if that's
where your cap3 is installed)
3. The run() method does this:

my $commandstring = $exe . $param_string . " $infilename1";

but at least for the version of cap3 I'm using, you need to put the
$param_string _after_ the $infilename1 for it to work.  Once all these
things are corrected it worked for me and correctly passed the -y 150 to
cap3 when new() was called as shown above.

Jonathan



On Wed, May 6, 2009 at 11:23 AM, Kevin Brown <Kevin.M.Brown at asu.edu>
wrote:

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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