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scripts/assign-colors updates for mpox #55

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scripts/assign-colors updates for mpox #55

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d82b968
scripts/assign-colors: Add `--ignore-categories` option
joverlee521 Jul 8, 2025
f561770
scripts/assign-colors: Add `--force-include-categories` option
joverlee521 Jul 9, 2025
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16 changes: 14 additions & 2 deletions scripts/assign-colors
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ if __name__ == '__main__':

parser.add_argument('--ordering', type=str, required=True,
help="""Input TSV file defining the color ordering where the first
column is the field and the second column is the trait in that field.
column is the category and the second column is the trait in that category.
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@jameshadfield jameshadfield Jul 9, 2025

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[sidebar] I always struggle to name these things, especially when they have a value attached. Category / trait / value seems pretty good.

Blank lines are ignored. Lines starting with '#' will be ignored as comments.""")
parser.add_argument('--color-schemes', type=str, required=True,
help="Input color schemes where each line is a different color scheme separated by tabs.")
Expand All @@ -23,6 +23,16 @@ if __name__ == '__main__':
metadata. If the metadata includes a 'focal' column that only contains
boolean values, then restrict colors to traits for rows where 'focal'
is set to True.""")
parser.add_argument('--ignore-categories', type=str, default=[], nargs='*',
help="""Do not create colors for these categories even if they are
included in the metadata and ordering TSV. This is useful for ignoring
categories in specific builds even if they share the same default
ordering TSV.""")
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@jameshadfield jameshadfield Jul 9, 2025 •
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[discussion] An alternative UI would be to have ordering TSVs for different categories and then allow multiple --ordering values. Thoughts? Do we plan on vendoring some big ordering list, or copy-paste across repos?

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@joverlee521 joverlee521 Jul 9, 2025

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I suspect that there will be some overlap in ordering but not always. Even for division/location, the ordering may depend on where the pathogen is circulating? I'd think each pathogen would have it's own ordering TSV to support their own uses.

parser.add_argument('--force-include-categories', type=str, default=[],nargs='*',
help="""Force include all color orderings for these categories even if
there are traits not included in the metadata TSV. This is useful for
creating colorings for traits not (yet) present in metadata to solve
bootstrapping issue.""")
Comment on lines +31 to +35
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@jameshadfield jameshadfield Jul 9, 2025

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I have no idea what a "bootstrapping issue" is. I suspect this is a valid use-case, but perhaps adjust the argument help text?

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@joverlee521 joverlee521 Jul 9, 2025

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To be honest, I'm not 100% sure what the bootstrapping issue is either, I was just trying to support the changes added in mpox from nextstrain/mpox@f9221c0.

parser.add_argument('--output', type=str, required=True,
help="Output colors TSV file to be passed to augur export.")
args = parser.parse_args()
Expand All @@ -42,6 +52,8 @@ if __name__ == '__main__':
else:
name = array[0]
trait = array[1]
if name in args.ignore_categories:
continue
if name not in assignment:
assignment[name] = [trait]
else:
Expand All @@ -53,7 +65,7 @@ if __name__ == '__main__':
if args.metadata:
metadata = pd.read_csv(args.metadata, delimiter='\t')
for name, trait in assignment.items():
if name in metadata:
if name in metadata and name not in args.force_include_categories:
if 'focal' in metadata and metadata['focal'].dtype == 'bool':
focal_list = metadata.loc[metadata['focal'], name].unique()
subset_focal = [x for x in assignment[name] if x in focal_list]
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