rescript merge-taxa secondary selection criteria

[Nicholas_Bokulich]

Everyone is right:

@colinbrislawn

As far as I can tell, in the event of a tie, the second option is chosen.

Correct

@SoilRotifer

There are pair-wise comparisons being made across the taxonomic lineages

i.e., when using len mode this action iterates across the taxonomies and compares each one to the current "winner".

So when there are only two taxonomies being compared, the second one given "wins" if there is a tie. If using 3 or more taxonomies, this gets a little more complicated, and order of precedence (for tiebreaking) is given in the reverse order that taxonomies are listed (so first gets lowest precedence, second beats first in a tie, third beats second in a tie, etc).

@SoilRotifer

@smayne11

I would like to merge taxonomies created through two classification methods on the same dataset, but giving one of the classification methods preference when classification length is equal.

I really like this, as it ties in with my idea of leveraging an ensemble approach for taxonomic classification.

Exactly! That's what this action was originally written for, to allow different types of ensemble classifications, e.g., when combining resutls from different taxonomic classifiers.

So @smayne11 to get the functionality that you desire, you would use this action like so:

qiime rescript merge-taxa \
    --i-data second-best-taxonomy.qza your-favorite-taxonomy.qza \
    --o-merged-data consensus-taxonomy.qza

Good luck!