[BioRuby] Gene duplications GSoC project: answers to some of your questions
Christian M Zmasek
czmasek at burnham.org
Thu Jun 17 22:49:12 UTC 2010
Hi, Sara:
Regarding some of your questions posted on
http://wiki.github.com/srayburn/bioruby/gsoc-2010-implementing-sdi-project-updates
Re: "Right now initialization loads from a hard coded file. I need to
make this flexible so that trees can come from any file or from a
previously loaded tree object":
The input of the algoruthm(s) should be tree-objects, reading the trees
should not be part of the algorithm implementation.
Clearly, for testing you need to read the trees from files, but this
should be implemented in your test code, not as part of the algorithm
implementation itself.
Re: "The names of leaf nodes: how standard are they? Is there a standard
format here? I’m going to look at example trees from the forester
implementation to get ideas about this. If I’m still stumped I’ll check
with my mentors."
No there is no standard. The only question for the purpose of this
algorithm do they match or not. I.e. they names could just numbers,
common names, or scientific names.
Hope this helps,
Christian
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