[Bioperl-guts-l] [BioPerl - Bug #3075] Bio::Tools::Run::Alignment::MAFFT: not able to specify alignment run parameters

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Thu Mar 17 07:54:24 EDT 2011

Issue #3075 has been updated by Mathias Walter.

I've rewritten the parameter handling so that it can be used like in TCOFFEE or ClustalW.

One minor problem is still left. I'll provide a patch soon.
Bug #3075: Bio::Tools::Run::Alignment::MAFFT: not able to specify alignment run parameters

Author: Oliver Niehuis
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Unclassified
Target version: 1.6 branch


this is request to update the Bio::Tools::Run::Alignment::MAFFT module. I tried to run the alignment program MAFFT with the Bio::Tools::Run::Alignment::MAFFT module, and while it is possible to run MAFFT with the default parameters, the module, in its current form, apparently does not allow to set specific parameters. For example: --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 posted the problem to the bioperl-l-request at lists.open-bio.org list server and got some useful feedback. However, the problem has not been solved yet. Since I was encouraged to submit the problem as a bug at http://bugzilla.bioperl.org, I am reporting the problem here. I hope it is not out of space.

Best wishes,

Best wishes,

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