7cef739b740764fdd246db8182072142c1a6c011
lrnassar
  Mon Jun 17 15:23:09 2024 -0700
Chaning up some of the colors for the ENIGMA hub tracks as advised by Anna.

diff --git src/hg/makeDb/scripts/enigma/BRCAmla.py src/hg/makeDb/scripts/enigma/BRCAmla.py
index b26cd8d..13524f3 100644
--- src/hg/makeDb/scripts/enigma/BRCAmla.py
+++ src/hg/makeDb/scripts/enigma/BRCAmla.py
@@ -1,35 +1,35 @@
 import subprocess
 
 def bash(cmd):
     """Run the cmd in bash subprocess"""
     try:
         rawBashOutput = subprocess.run(cmd, check=True, shell=True,\
                                        stdout=subprocess.PIPE, universal_newlines=True, stderr=subprocess.STDOUT)
         bashStdoutt = rawBashOutput.stdout
     except subprocess.CalledProcessError as e:
         raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output))
     return(bashStdoutt)
 
 def assignRGBcolorByLR(LR):
     LR = float(LR)
     if LR > 2.08:
-        itemRgb = '255,0,0'
+        itemRgb = '128,64,13' #brown
     elif LR <=0.48:
-        itemRgb = '0,128,0'
+        itemRgb = '252,157,3' #orange
     else:
-        itemRgb = '91,91,91'
+        itemRgb = '91,91,91' #grey
     return(itemRgb)
 
 def assignACMGcode(LR):
     LR = float(LR)
     if LR > 2.08 and LR <= 4.3:
         ACMGcode = 'PP4 - Pathogenic - Supporting'
     elif LR > 4.3 and LR <= 18.7:
         ACMGcode = 'PP4 - Pathogenic - Moderate'
     elif LR > 18.7 and LR <= 350:
         ACMGcode = 'PP4 - Pathogenic - Strong'
     elif LR > 350:
         ACMGcode = 'PP4 - Pathogenic - Very strong'
     elif LR <= .48 and LR > .23:
         ACMGcode = 'BP5 - Benign - Supporting'
     elif LR <= .22 and LR > .05: