Bio::Tools::Run::Alignment::MAFFT: not able to specify alignment run parameters

[cjfields]

---

Author Name: Oliver Niehuis (Oliver Niehuis)
Original Redmine Issue: 3075, https://redmine.open-bio.org/issues/3075
Original Date: 2010-05-10
Original Assignee: Bioperl Guts

---

Hi,

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@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,
Oliver

Best wishes,
Oliver

[cjfields]

---

Original Redmine Comment
Author Name: Mathias Walter
Original Date: 2011-03-17T11:54:24Z

---

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.