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Add default clade color #73

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merged 2 commits into from
Nov 28, 2023
Merged

Add default clade color #73

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c9323a7
Remove excess whitespace
joverlee521 Nov 28, 2023
fec15d1
modify-lineage-colours-and-order: Add default clade color
joverlee521 Nov 28, 2023
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21 changes: 17 additions & 4 deletions scripts/modify-lineage-colours-and-order.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,11 @@
import numpy as np
import colorsys


# Color for clades that lack clade definition, but we don't want to group with 'other'
DEFAULT_CLADE_COLOR = '#474747'


def order_lineages(lineages, aliasor):
"""
Order input lineages by using their full uncompressed lineage & converting to a sortable form
Expand Down Expand Up @@ -40,7 +45,15 @@ def clade_colors(variants, clade_definitions):
except KeyError:
if v!='other':
missing.add(v)
assert len(missing) == 0, f"Missing definitions for the following clades: {', '.join(missing)}"
defs.append([v, DEFAULT_CLADE_COLOR])

# TODO: Emit this to output file so it can be sent thru Slack notifications
if len(missing) > 0:
print(
f"Missing definitions for the following clades: {', '.join(missing)}.",
f"They have been assigned the default color {DEFAULT_CLADE_COLOR!r}"
)

return defs

def clade_display_names(variants, clade_definitions):
Expand All @@ -63,7 +76,7 @@ def colour_range(anchor, n):
lrange = np.linspace(anchor_hls[1]*1.2, anchor_hls[1], n)
srange = np.linspace(anchor_hls[2]*0.7, anchor_hls[2]*1.1, n)
rgb_range = [colorsys.hls_to_rgb(*hls) for hls in zip(hrange, lrange, srange)]
def clamp(x):
def clamp(x):
return int(max(0, min(x, 255)))
return [f"#{clamp(rgb[0]):02x}{clamp(rgb[1]):02x}{clamp(rgb[2]):02x}" for rgb in rgb_range]

Expand All @@ -77,7 +90,7 @@ def colourise(lineages, aliasor, clade_definitions):
"""
clades = {lineage: lineage_to_clade(lineage, aliasor, 'other', clade_definitions)
for lineage in lineages}

colours = []

for clade in list(set(clades.values())):
Expand Down Expand Up @@ -124,4 +137,4 @@ def colourise(lineages, aliasor, clade_definitions):
print(f"Variant classification of {args.variant_classification}: no post-processing of JSON")

with open(args.output, 'w') as fh:
json.dump(data, fh, indent=None)
json.dump(data, fh, indent=None)
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