[BioRuby] Options for ClustalW wrapper
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Tue Jul 29 10:01:42 UTC 2008
Hi,
On Tue, 29 Jul 2008 08:46:55 +0200
Marc Hoeppner <marc.hoeppner at molbio.su.se> wrote:
> Hi,
>
> I am sorry if there is a good tutorial for this somewhere, but I
> couldn't find it. The API didn't help either, so here is my question:
>
> I want to use ClustalW to create an alignment using
>
> factory = Bio::ClustalW.new
>
> How exactly can I pass options to ClustalW here? Like gap open penalty
> and such?
Command-line options passed to clustalw can be set when creating
factory object, or later by using Bio::Clustalw#options method.
#-----------------------------------------------------------
factory = Bio::ClustalW.new('clustalw',
[ '-kimura', '-endgaps' ])
gap_open = 1.0
factory.options.push "-gapopen=#{gap_open}"
gap_ext = 1.0
factory.options.push "-gapext=#{gap_ext}"
more_options = [ '-nopgap', '-nohgap' ]
factory.options.concat more_options
p factory.options
seqs = [ 'atgaaaca', 'aagaaca', 'acgaaca', 'acgaaacg' ]
seqs = seqs.collect{ |x| Bio::Sequence::NA.new(x) }
result = factory.query(seqs)
print result.raw
#-----------------------------------------------------------
List of command line options of clustalw can be seen
by executing clustalw with '-help' option.
% clustalw -help
Cheers,
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
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