don't make index (#675)

* don't make index

* updated webcolors broke

jcvi/formats/gff.py

@@ -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):
@@ -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)

jcvi/utils/webcolors.py

@@ -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):
@@ -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)