[BioRuby] Problem running HMMER from bioruby
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Fri Jul 18 03:15:45 UTC 2008
Hi,
On Thu, 17 Jul 2008 20:10:11 +0300
"George Githinji" <georgkam at gmail.com> wrote:
> Hi!
> What could possibly be wrong with this code for running a hmm search the
> bioruby way?
>
> hmmfile = "/home/george/NetBeansProjects/pfvsa/public/hmms/pfVSAs.hmm"
>
> #the bioruby way
> seq_to_search ="/home/george/sequences/sequences.fasta"
> factory = Bio::HMMER.new('hmmpfam',hmmfile,seq_to_search)
> report = factory.query
> puts report.class
>
> I am getting this error
>
> /usr/lib/ruby/1.8/shellwords.rb:30:in `shellwords': Argument must be a
> string (ArgumentError)
> from
> /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/hmmer.rb:70:in
> `initialize'
This is caused by a bug in bioruby.
For a workaround, set option as a string. e.g.
factory = Bio::HMMER.new('hmmpfam',hmmfile,seq_to_search, '')
To fix the bug, a patch is available.
====================================================
--- a/lib/bio/appl/hmmer.rb
+++ b/lib/bio/appl/hmmer.rb
@@ -64,7 +64,7 @@ class HMMER
@output = ''
begin
- @options = opt.to_ary
+ @options = options.to_ary
rescue NameError #NoMethodError
# backward compatibility
@options = Shellwords.shellwords(options)
====================================================
--
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
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