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Augur export converts literals to lower case in its stderr output - which is probably not what we want
Expected behavior
Literals are output as they are, not changing case.
How to reproduce
Steps to reproduce the current behavior:
Include some extra literals in a colors file, including upper case in non-initial position, e.g. 21L
Run augur export with --colors
Observe log message
$ augur export v2 --tree builds/wuhan/tree.nwk --metadata builds/wuhan/metadata_with_bloom_scores.tsv --node-data builds/wuhan/branch_lengths.json builds/wuhan/muts.json builds/wuhan/clades_display.json builds/wuhan/clades.json builds/wuhan/clades_nextstrain.json builds/wuhan/clades_who.json builds/wuhan/internal_pango.json \
--colors builds/wuhan/colors.tsv --auspice-config profiles/clades/wuhan/auspice_config.json --title 'SARS-CoV-2 phylogeny' --description profiles/clades/description.md --include-root-sequence-inline --minify-json --output auspice/wuhan/auspice_raw.json
Validating schema of 'builds/wuhan/muts.json'...
Validating config file profiles/clades/wuhan/auspice_config.json against the JSON schema
Validating schema of 'profiles/clades/wuhan/auspice_config.json'...
WARNING: Requested color-by field 'placement_priors' does not exist and will not be used as a coloring or exported.
WARNING: These values fortrait clade_membership were not specifiedin the colors file you provided:
21k, 21f, 20f, 20h, 20b, 21m, 19a, 20i, 20c, recombinant, 21e, 21g, 20g, 20a, 21j, 20e, 20j, 21d, 21i, 21a, 20d, 19b, 21b, 21c, 21h.
Auspice will create colors for them.
WARNING: These values fortrait clade_who were not specifiedin the colors file you provided:
recombinant.
Auspice will create colors for them.
WARNING: These values fortrait clade_nextstrain were not specifiedin the colors file you provided:
21k, 21f, 20f, 20h, 20b, 21m, 19a, 20i, 20c, recombinant, 21e, 21g, 20g, 20a, 21j, 20e, 20j, 21d, 21i, 21a, 20d, 19b, 21b, 21c, 21h.
Auspice will create colors for them.
Validating produced JSON
Validating schema of 'auspice/wuhan/auspice_raw.json'...
Validating that the JSON is internally consistent...
WARNING: The filter "new_node" does not appear as a property on any tree nodes.
Validation of 'auspice/wuhan/auspice_raw.json' succeeded, but there were warnings you may want to resolve.
warn(f"These values for trait {key} were not specified in the colors file you provided:\n\t{', '.join(trait_values_unseen)}.\n\tAuspice will create colors for them.")
returncoloring
warn(f"You've supplied a colors file with information for {key} but none of the values found on the tree had associated colors. Auspice will generate its own color scale for this trait.")
Current Behavior
Augur export converts literals to lower case in its stderr output - which is probably not what we want
Expected behavior
Literals are output as they are, not changing case.
How to reproduce
Steps to reproduce the current behavior:
21L
--colors
Note this line:
the input colors were
21K
not21k
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