[Bioperl-l] Bio::Tools::Run::Alignment::MAFFT - specifyingalignment parameters

[Mark A. Jensen]

Hi Oliver,
This module looks like it needs some updating. Here's a hack
that should make it work (or at least prevent that exception);
put the following lines before the new() call:

push @Bio::Tools::Run::Alignment::MAFFT::MAFFT_PARAMS, 'MAXITERATE';
push @Bio::Tools::Run::Alignment::MAFFT::MAFFT_SWITCHES, 'LOCALPAIR';
$Bio::Tools::Run::Alignment::MAFFT::OK_FIELD{MAXITERATE} = 1;
$Bio::Tools::Run::Alignment::MAFFT::OK_FIELD{LOCALPAIR} = 1;

HTH,
Mark

----- Original Message ----- 
From: "Dr. Oliver Niehuis" <O.Niehuis.zfmk at uni-bonn.de>
To: <bioperl-l at lists.open-bio.org>
Sent: Friday, May 07, 2010 2:34 AM
Subject: [Bioperl-l] Bio::Tools::Run::Alignment::MAFFT - specifyingalignment 
parameters


> Hi,
>
> I have a question about how to specify parameters for the alignment  program 
> MAFFT via the Bio::Tools::Run::Alignment::MAFFT module. I  would like to run 
> MAFFT with the following alignment parameters:
>
> --maxiterate 1000 --localpair
>
> Having used TCOFFEE and the Bio::Tools::Run::Alignment::Tcoffee module 
> before, I specified the MAFFT run parameters as follows:
>
> @params = ('localpair', 'maxiterate' => 1000);
> $factory = Bio::Tools::Run::Alignment::MAFFT->new(@params);
>
> Unfortunately, this code causes an exception error:
>
> ------------- EXCEPTION -------------
> MSG: Unallowed parameter: LOCALPAIR !
> STACK Bio::Tools::Run::Alignment::MAFFT::AUTOLOAD /sw/lib/perl5/5.8.8/ 
> Bio/Tools/Run/Alignment/MAFFT.pm:211
> STACK Bio::Tools::Run::Alignment::MAFFT::new /sw/lib/perl5/5.8.8/Bio/ 
> Tools/Run/Alignment/MAFFT.pm:196
> STACK toplevel /Users/Oliver/Desktop/Orthologs/ 
> Generate_FASTA_files_of_orthologs.pl:55
> -------------------------------------
>
> I can align sequences with MAFFT via Bio::Tools::Run::Alignment::MAFFT 
> module, but only when leaving the @params array empty; MAFFT then runs  with 
> the default parameters.
>
> Has anyone an idea how I can specify run parameters for MAFFT via the 
> Bio::Tools::Run::Alignment::MAFFT module?
>
> Any help is much appreciated!
>
> Best wishes,
> Oliver
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