34b96568359c6125704a1eb7455dd39e99744a72
chmalee
  Thu Jul 2 10:36:03 2020 -0700
Fix up the ClinGen Dosage and CNV colors and mouseovers, refs #24818,#25562

diff --git src/hg/utils/otto/clinGen/processClinGenDosage.py src/hg/utils/otto/clinGen/processClinGenDosage.py
index 3563fec..acd48c7 100755
--- src/hg/utils/otto/clinGen/processClinGenDosage.py
+++ src/hg/utils/otto/clinGen/processClinGenDosage.py
@@ -63,45 +63,45 @@
                     print("duplicate info for gene symbol: '%s'" % (geneSymbol))
                     sys.exit(1)
             except KeyError:
                 extraInfo[geneSymbol] = {}
                 for keyName,ix in zip(extraFieldList[1:],range(len(extraFieldList[1:]))):
                     try:
                         if fieldMatch.match(keyName):
                             continue
                         extraInfo[geneSymbol][keyName] = extra[ix]
                     except IndexError:
                         sys.exit(1)
 
 def getColor(bed, dosageType):
     """Return the shade of the item according to it's variant type."""
     if dosageType == "haplo":
-        if bed["score"] == -1: return "128,128,128"
-        if bed["score"] == 0: return "191,191,191"
-        if bed["score"] == 1: return "191,115,115"
-        if bed["score"] == 2: return "191,93,96"
-        if bed["score"] == 3: return  "255,51,0"
-        if bed["score"] == 30: return "160,136,246"
-        if bed["score"] == 40: return "255,204,204"
+        if bed["score"] == -1: return "218,215,215"
+        if bed["score"] == 0: return "130,128,128"
+        if bed["score"] == 1: return "232,104,111"
+        if bed["score"] == 2: return "218,44,55"
+        if bed["score"] == 3: return  "180,3,16"
+        if bed["score"] == 30: return "137,93,189"
+        if bed["score"] == 40: return "238,146,148"
     if dosageType == "triplo":
-        if bed["score"] == -1: return "128,128,128"
-        if bed["score"] == 0: return "191,191,191"
-        if bed["score"] == 1: return "180,198,231"
-        if bed["score"] == 2: return "142,169,219"
-        if bed["score"] == 3: return "48,84,150"
-        if bed["score"] == 30: return "160,136,246"
-        if bed["score"] == 40: return "217,255,242"
+        if bed["score"] == -1: return "218,215,215"
+        if bed["score"] == 0: return "130,128,128"
+        if bed["score"] == 1: return "88,131,211"
+        if bed["score"] == 2: return "41,78,174"
+        if bed["score"] == 3: return "17,44,138"
+        if bed["score"] == 30: return "137,93,189"
+        if bed["score"] == 40: return "122,165,211"
 
 def getMouseover(bed, dosageType):
     """Return the mouseOver string for this bed record."""
     ret = "Gene: %s" % bed["name"]
     if dosageType == "triplo":
         ret += ", Triplosensitivity: "
     else:
         ret += ", Haplosensitivity: "
     ret += "%s - %s" % (bed["score"], scoreExplanation[bed["score"]])
     return ret
 
 def dumpBedLines(dosageType):
     """Write out the bed lines, with the same number of fields in each line."""
     oppMatchStr = "triplo" if dosageType == "haplo" else "haplo|loss"
     extraFields = [x for x in extraFieldList if not re.match(oppMatchStr, x, re.I) and x != "Gene Symbol" and x != "Genomic Location"]