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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looks useful! Thanks. would it be easy to have a flag to activate it or its computation and the increase in the orthoxml file size would be negligible? |
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extra size is quite fine: 2 additional lines per sub-hog (one for tcs score, on for implied loss). for the computation, I think I can benchmark this on a medium size dataset. will let you know. having a flag to active/deactivate would certainly be possible. |
Adds --store-completeness-score/--store-implied-losses-score/--store-tcs-score options to fastoma-infer-subhogs (wired through FastOMA.nf as store_completness_score/store_implied_losses_score/store_tcs_score params) so score computation can be toggled per run. collect_subhogs now looks ahead at the first HOG in the pickle folder to only write scoreDef entries for scores actually present in the run's output, instead of always writing all three. compute time for score computation is tracked during the to_orthoxml() call. Serialization is generally quick, score computation uses roughly 40% of the time.
The previous --store_*_score params (default true) were missing from nextflow_schema.json, so nf-schema parsed CLI-supplied values as plain strings instead of booleans -- a non-empty string is truthy in Groovy, so --store_tcs_score false never actually disabled anything. Switch to --disable_*_score (default false): setting the flag means the user actively wants to disable the score, so bare presence of the flag conveys the intent without needing a boolean value at all.
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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.