4bf8cd5b339e46ed05d34677f0fed28eb2b03463
lrnassar
  Thu May 26 17:14:43 2022 -0700
Setting MTR track to QA ready. Choosing new .ra setting to highlight low values, updating the make script, and improving the desc page. Refs #29152

diff --git src/hg/makeDb/scripts/mtr/buildMTRbedTrack.py src/hg/makeDb/scripts/mtr/buildMTRbedTrack.py
index cddf1e7..898abc5 100644
--- src/hg/makeDb/scripts/mtr/buildMTRbedTrack.py
+++ src/hg/makeDb/scripts/mtr/buildMTRbedTrack.py
@@ -1,29 +1,29 @@
 from collections import OrderedDict
 
 #chr20   68354   A       C       ENST00000382410 2       missense_variant        16      0.75    0.725   1.034   1       70.701
 #Chromosome_name-Genomic_position-ref-alt-Feature-Protein_position-Consequence-missyn_tally-mtr_obs-mtr_exp-MTR-FDR-MTR_centile
 mtrFile = open("/hive/data/outside/mtr/mtrUcsc.txt",'r')
 outFile = open("/hive/data/outside/mtr/mtr2.bed",'w')
 
-#Items in the top 25centile = red, middle 50 = black, lower 25 = green, and no score = blue
+#Items in the bottom 25centile = red, middle 50 = black, top 25 = green, and no score = blue
 def assignRGBcolorByMTRcentile(mtrCentile):
     """Assign color based on mtr percentile"""
     
-    if float(mtrCentile) > .75:
+    if float(mtrCentile) < 25:
         itemRgb = '255,0,0'
-    elif float(mtrCentile) < .25:
+    elif float(mtrCentile) > 75:
         itemRgb = '0,128,0'
     else:
         itemRgb = '0,0,0'
     return(itemRgb)
 
 mtrScoreDic = OrderedDict()
 
 prevChrom = ""
 for line in mtrFile:
     line = line.rstrip().split("\t")
     chrom = line[0]
     if prevChrom != chrom:
         print("On new chrom: "+chrom)
     chromStart = int(line[1])-1
     chromEnd = int(line[1])