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nhoffman / bioy

Tools for NGS sequence analysis and bacterial classification
GNU General Public License v3.0
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054 ref rank #56

Closed tyleraland closed 8 years ago

tyleraland commented 8 years ago

"include-ref-rank" argument, pulls in rank-level taxonomic ID and name from taxonomy and includes it in every details row.

Can be used like: --include-ref-rank species --include-ref-rank species_group --include-ref-rank genus to include information from multiple ranks

TODO: Tests?

crosenth commented 8 years ago

Tests would be good and also update the CHANGELOG.rst

tyleraland commented 8 years ago

I'm not really sure what's worth testing.

I could test for the obvious, that if I pass in "--include-ref-rank $RANK" that "$RANK_id,$RANK_name" are in the output file (for one or two particular ranks), but this doesn't seem particularly useful to me.

I could test for failure -- If I ask for "--include-ref-rank unknown", then it will expectedly fail. Alternatively, I could write it so that it fails gracefully and then test for that, although I think it makes more sense to fail noisily if the desired rank is not in the taxonomy.

Unless one feels stongly that one of these tests should be implemented, I think merging it without writing tests is most appropriate, given our usual development style.