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don't make index #675

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merged 2 commits into from
Jun 8, 2024
Merged

don't make index #675

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0cfda75
don't make index
Jun 8, 2024
893d468
updated webcolors broke
tanghaibao Jun 8, 2024
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4 changes: 2 additions & 2 deletions jcvi/formats/gff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2829,9 +2829,9 @@ def note(args):
if type:
type = type.split(",")

g = make_index(gffile)
exoncounts = {}
if opts.exoncount:
g = make_index(gffile)
for feat in g.features_of_type("mRNA"):
nexons = 0
for c in g.children(feat.id, 1):
Expand All @@ -2851,7 +2851,7 @@ def note(args):
if AED is not None and float(g.attributes["_AED"][0]) > AED:
continue
keyval = [g.accn] + [
",".join(g.attributes[x]) for x in attrib if x in g.attributes
",".join(g.attributes.get(x, ["nan"])) for x in attrib
]
if exoncounts:
nexons = exoncounts.get(g.accn, 0)
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7 changes: 4 additions & 3 deletions jcvi/utils/webcolors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@
import numpy as np

from skimage.color import rgb2lab, deltaE_cmc
from webcolors import CSS3_HEX_TO_NAMES, hex_to_rgb
from webcolors._definitions import _CSS3_NAMES_TO_HEX
from webcolors import hex_to_rgb


def color_diff(rgb1, rgb2):
Expand All @@ -38,8 +39,8 @@ def closest_color(requested_color):
"""
logging.disable(logging.DEBUG)
colors = []
for key, name in CSS3_HEX_TO_NAMES.items():
diff = color_diff(hex_to_rgb(key), requested_color)
for name, hex in _CSS3_NAMES_TO_HEX.items():
diff = color_diff(hex_to_rgb(hex), requested_color)
colors.append((diff, name))
logging.disable(logging.NOTSET)
_, min_color = min(colors)
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