89e9ea11b4ddd52983382a8731503dbb82421ca6
lrnassar
  Thu Nov 7 17:56:00 2024 -0800
Changing the track to have 5 decimals, feedback from Melissa.

diff --git src/hg/makeDb/scripts/enigma/BRCAmla.py src/hg/makeDb/scripts/enigma/BRCAmla.py
index 5e54d0a..68da10e 100644
--- src/hg/makeDb/scripts/enigma/BRCAmla.py
+++ src/hg/makeDb/scripts/enigma/BRCAmla.py
@@ -219,56 +219,56 @@
         ACMGcode = 'BP5 - Benign - Supporting'
     elif LR <= .22 and LR > .05:
         ACMGcode = 'BP5 - Benign - Moderate'
     elif LR <= .04 and LR > .00285:
         ACMGcode = 'BP5 - Benign - Strong'
     elif LR <= 0.00285:
         ACMGcode = 'BP5 - Benign - Very strong'
     else:
 #         print("This code did not match: "+str(LR))
         ACMGcode = "Not informative"
     return(ACMGcode)
 
 def checkVarAndWriteToLine(potentialDataset,combinedLRdic,variant,dataset,listOfValues,lineToWrite):
     if dataset in combinedLRdic[variant].keys():
         if potentialDataset in combinedLRdic[variant][dataset].keys():
-            listOfValues.append(str(round(combinedLRdic[variant][dataset][potentialDataset],3)))
+            listOfValues.append(str(round(combinedLRdic[variant][dataset][potentialDataset],5)))
         else:
             listOfValues.append("NULL")
     return(lineToWrite)
 
 def createOutputBedLine(combinedLRdic,vcfVarCoords):
     outputBedFile = open("/hive/data/inside/enigmaTracksData/outputBedFile.bed",'w')
     n=0
     for variant in combinedLRdic.keys():
         ACMGcode = assignACMGcode(combinedLRdic[variant]["combinedLRscore"])
         _mouseOver = "<b>HGVSc:</b> "+variant+"<br>"+\
-            "<b>Combined LR:</b> "+str(round(combinedLRdic[variant]["combinedLRscore"],3))+\
+            "<b>Combined LR:</b> "+str(round(combinedLRdic[variant]["combinedLRscore"],5))+\
             "<br><b>ACMG Code:</b> "+ACMGcode
         itemRGB = assignRGBcolorByLR(combinedLRdic[variant]["combinedLRscore"])
 
         if variant in vcfVarCoords.keys():
             #first three fields chrom, chromStart, chromEnd- then next 5 standard bed fields
             lineToWrite = ("\t".join(vcfVarCoords[variant])+\
             "\t"+variant+"\t0\t.\t"+"\t".join(vcfVarCoords[variant][1:])+\
-            "\t"+itemRGB+"\t"+str(round(combinedLRdic[variant]["combinedLRscore"],3))+"\t"+\
+            "\t"+itemRGB+"\t"+str(round(combinedLRdic[variant]["combinedLRscore"],5))+"\t"+\
             ACMGcode+"\t")
 
             #Add the combined LRs
             for LRcombined in ["familyLRcombined","coocurrenceLRcombined","segregationLRcombined","pathologyLRcombined","caseControlLRcombined"]:
                 if LRcombined in combinedLRdic[variant].keys():
-                    lineToWrite = lineToWrite+str(round(combinedLRdic[variant][LRcombined],3))+"\t"
+                    lineToWrite = lineToWrite+str(round(combinedLRdic[variant][LRcombined],5))+"\t"
                 else:
                     lineToWrite = lineToWrite+"\t"
 
             for dataset in ['caputoVarsDic','parsonsVarsDic','liVarsDic','eastonVarsDic']:
                 if dataset == 'caputoVarsDic':
                     listOfValues = []
                     for potentialDataset in ["familyLR","coocurrenceLR","segregationLR","pathologyLR"]:
                         lineToWrite = checkVarAndWriteToLine(potentialDataset,combinedLRdic,variant,dataset,listOfValues,lineToWrite)
                     lineToWrite = lineToWrite+",".join(listOfValues)+'\t'
                 elif dataset == 'parsonsVarsDic':
                     listOfValues = []
                     for potentialDataset in ["familyLR","coocurrenceLR","segregationLR","pathologyLR","caseControlLR"]:
                         lineToWrite = checkVarAndWriteToLine(potentialDataset,combinedLRdic,variant,dataset,listOfValues,lineToWrite)
                     lineToWrite = lineToWrite+",".join(listOfValues)+'\t'
                 elif dataset == 'liVarsDic':