[BioRuby] CodeML wrapper for BioRuby

Naohisa GOTO ngoto at gen-info.osaka-u.ac.jp
Fri Aug 15 11:15:09 UTC 2008


It seems good. It will be included in BioRuby.

In my machine, a test was failed.
Can you fix the problem?
$ ruby test/unit/bio/appl/test_codeml.rb
Loaded suite test/unit/bio/appl/test_codeml
Finished in 0.032717 seconds.

  1) Failure:
test_correct_options_should_be_loaded(Bio::TestConfigFileUsage) [test/unit/bio/appl/test_codeml.rb:87]:
<"/xxxxx/ngoto/work/test/data/codeml/abglobin.aa"> expected but was

7 tests, 9 assertions, 1 failures, 0 errors
(some part of file path is masked with "xxxxx")

On Wed, 13 Aug 2008 16:34:20 +0100
"Michael Barton" <mail at michaelbarton.me.uk> wrote:

> Hi,
> CodeML is a common tool for estimating evolutionary rate of protein encoding
> sequences, and is part of the PAML package. I've created a codeml wrapper
> and two parsers. Unit tests are also included. The code is in a Github fork
> in BioRuby. The fork is located here
> http://github.com/michaelbarton/bioruby/tree/master
> I like to suggested that it for inclusion in the main BioRuby branch.
> Thanks
> Mike
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