sourmash
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specifying multiple lineages for `sourmash tax` commands
for sourmash tax
, specify multiple taxonomy files like so:
sourmash tax annotate -g GATHER.csv --taxonomy DB_1.csv DB_2.csv
Here, DB_1
and DB_2
taxonomies will be loaded, with DB_2
overwriting any shared identifiers.
The following command is "valid" but does NOT have the same function:
sourmash tax annotate -g GATHER.csv --taxonomy DB_1.csv --taxonomy DB_2.csv
Here, we only read DB_2
and DB_1
is ignored entirely.
strikes me as a bug. this can be dealt with easily in argparse.
Adding action="extend" should handle this nicely. Will PR later today.