[BioRuby] Parsing MSF alignment file

Naohisa GOTO ngoto at gen-info.osaka-u.ac.jp
Mon Apr 13 12:54:54 UTC 2009


On Mon, 13 Apr 2009 13:16:00 +0900
Fredrik Johansson <fredjoha at bioreg.kyushu-u.ac.jp> wrote:

> I tried to parse an alignment file given in the MSF format by using 
> Bio::GCG::Msf. It turned out though that points/dots (.) were used as a 
> gap character in the alignment and that can't be handled by 
> Bio::GCG::Msf. So, for what it's worth, I made these changes to 
> bio/appl/gcg/msf.rb:

Thank you very much.  Do you mean that Bio::GCG::Msf fails to
parse an alignment that contain two contiguous gaps (..) in the
end of a line?  This is a bug, and the patch will soon be
applied to the git repository. 

> $ diff msf.rb.old msf.rb.new

In the next time, please use "diff -u" (unified context format).


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

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