Tcs and implied loss scores - #93
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adds TCS score according to reference implementation. adds implied loss score computing the nr of implied loss of a (sub)HOG.
adds unittests about the score calculation and update the nf-test output with the addtional score lines
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@sinamajidian what do you think about the tcs score? should we include it like this? (see my comment in the toplevel description.) |
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attempt to include two more scores into the orthoxml:
ImpliedLosses: number of implied gene loss for the subhog underneath the which stores the score.
TCSScore: Taxonomic congruence score as defined in the FoldTree publication. As taxonomy, the species tree given to FastOMA is used. We normalize the score with the number of genes. However, this does NOT mean the score is in the (0,1) range. This is also reflected when you run the example data. The TCS score can be <1 for a perfectly congruent HOG without any loss/gains.