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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Mon May 19 22:07:47 EDT 2008


Hi Steve,

The _set_from_args() method is implemented in the Bio::Root::RootI 
class, which is a module from the bioperl (core) distribution, not from 
bioperl-run. In order to use any of the bioperl-run wrappers you'll need 
to install the core bioperl distribution as well.

Hope this helps.

Regards,
Mauricio.

sbeckstrom at tgen.org wrote:
> 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
>>>
>>>
> 
> 
> 
> 
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> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM


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