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/buildMTRwigTracks.py src/hg/makeDb/scripts/mtr/buildMTRwigTracks.py
index ba5f894..18fce88 100644
--- src/hg/makeDb/scripts/mtr/buildMTRwigTracks.py
+++ src/hg/makeDb/scripts/mtr/buildMTRwigTracks.py
@@ -1,68 +1,68 @@
 from collections import OrderedDict
 
 mtrFile = open("/hive/data/outside/mtr/mtrflatfile_2.0.txt",'r')
 aWig = open("/hive/data/outside/mtr/a.wig",'w')
 cWig = open("/hive/data/outside/mtr/c.wig",'w')
 gWig = open("/hive/data/outside/mtr/g.wig",'w')
 tWig = open("/hive/data/outside/mtr/t.wig",'w')
 
 def writeOutToWig(positionDic,fileNames):
     for key in positionDic.keys():
         try: prevPos
         except:
             prevPos = False
         currentPos = key
         for base, fileName in zip(['A','C','T','G'], fileNames):
             if prevPos == False or int(currentPos)-1 != int(prevPos):
                 fileName.write("fixedStep chrom=%s start=%s step=1 span=1\n" % (positionDic[key]['chr'],currentPos))
-                if positionDic[key][base] == [] or max(positionDic[key][base]) == '':
+                if positionDic[key][base] == [] or min(positionDic[key][base]) == '':
                     fileName.write('0\n')
                 else:
-                    fileName.write(str(max(positionDic[key][base]))+"\n")
+                    fileName.write(str(min(positionDic[key][base]))+"\n")
             else:
-                if positionDic[key][base] == [] or max(positionDic[key][base]) == '':
+                if positionDic[key][base] == [] or min(positionDic[key][base]) == '':
                     fileName.write('0\n')
                 else:
-                    fileName.write(str(max(positionDic[key][base]))+"\n")                    
+                    fileName.write(str(min(positionDic[key][base]))+"\n")                    
         prevPos = currentPos
 
 for line in mtrFile:
     if line.startswith("Chromosome_name"):
         print("Skipped")
     else:
         try: prevChrom
         except:
             prevChrom = False
         lineSplit = line.split("\t")
         chrom = "chr"+lineSplit[0]
         pos = lineSplit[1]
         alt = lineSplit[3]
         mtr = lineSplit[0]
     
         if not prevChrom:
             positionDic = OrderedDict()
         
         elif chrom != prevChrom:
             print("Writing chrom: "+prevChrom)
             writeOutToWig(positionDic,[aWig,cWig,tWig,gWig])
             positionDic = OrderedDict()
     
         if pos not in positionDic.keys():
             positionDic[pos] = {}
             positionDic[pos]['C'] = []
             positionDic[pos]['A'] = []
             positionDic[pos]['G'] = []
             positionDic[pos]['T'] = []
             positionDic[pos]['chr'] = chrom
         
         positionDic[pos][alt].append(lineSplit[10])
         prevChrom = chrom
 
 print("Writing chrom: "+prevChrom)
 writeOutToWig(positionDic,[aWig,cWig,tWig,gWig])
                 
 mtrFile.close()
 aWig.close()
 cWig.close()
 tWig.close()
 gWig.close()