[Bioperl-l] Bio::Align::DNAStatistics

[sbeckstrom at tgen.org]

Hi Jason,

The problem seems to be specific to Clustalw.pm, with version listed here:
(# $Id: Clustalw.pm,v 1.53 2007/06/14 15:23:08 sendu Exp $)

Below is subroutine "new", which calls _set_from_args in line 409 of
Clustalw.pm:

sub new {
    my ($class, at args) = @_;
    my $self = $class->SUPER::new(@args);

    $self->_set_from_args(\@args, -methods => [@CLUSTALW_PARAMS,
                                               @CLUSTALW_SWITCHES,
                                               @OTHER_SWITCHES],
                                  -create => 1);
    
    return $self;
}

The error states that it cannot find the _set_from_args method.
And I cannot find a subroutine called _set_from_args in Clustalw.pm.
What am I missing?

Thanks,

Steve




On 5/16/08 4:15 PM, "Jason Stajich" <jason at bioperl.org> wrote:

> Sounds like an old bioperl version mixture, but I'm not sure, you'll
> need to let us know what version of bioperl you have installed.
> 
> Please include the mailing list in these types of questions so others
> can help.
> 
> -jason
> On May 15, 2008, at 1:49 PM, Steve Beckstrom-Sternberg wrote:
> 
>> Hi Jason,
>> 
>> I have bioperl-run installed and I am testing pairwise_kaks.PLS.
>> I am getting an error from Clustalw.pm, and it looks like this is
>> because
>> subroutine ³new² is calling a subroutine that is not there
>> (_set_from_args).
>> 
>> Here is the error:
>> 
>> ./pairwise_kaks.PLS
>> Can't locate object method "_set_from_args" via package
>> "Bio::Tools::Run::Alignment::Clustalw" at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm
>> line 409.
>> 
>> Here is the version of Clustalw.pm:
>> # $Id: Clustalw.pm,v 1.53 2007/06/14 15:23:08 sendu Exp $
>> 
>> 
>> Any direction on how to resolve this?
>> 
>> Thanks,
>> 
>> Steve
>> 
>>