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/BRCAfunctionalAssays.py src/hg/makeDb/scripts/enigma/BRCAfunctionalAssays.py
index 8f1857f..6731b64 100644
--- src/hg/makeDb/scripts/enigma/BRCAfunctionalAssays.py
+++ src/hg/makeDb/scripts/enigma/BRCAfunctionalAssays.py
@@ -5,52 +5,51 @@
     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)
 
 rawFilePath = "/hive/data/inside/enigmaTracksData/CSpec_BRCA12ACMG_Rules-Specifications_V1.1_Table-9_2023-11-22-1.txt"
 bash("tail -n +4 "+rawFilePath+" > /hive/data/inside/enigmaTracksData/CSpecDataMinusHeader.txt")
 rawFileNoHeader = open('/hive/data/inside/enigmaTracksData/CSpecDataMinusHeader.txt','r', encoding='latin-1')
 varsToConvertToVcf = open('/hive/data/inside/enigmaTracksData/varsToConvert.txt','w')
 
 def assignRGBcolor(assignedCode):
     if assignedCode == "PS3":
-        itemRgb = '255,0,0' #Red
+        itemRgb = '0,100,120' #Dark blue
     elif assignedCode == "BS3":
-        itemRgb = '0,128,0' #Green
+        itemRgb = '0,200,240' #Light blue
     elif assignedCode == "None":
         itemRgb = '0,0,0' #Black
     else:
         print("Error, no code match: "+assignedCode)
     return(itemRgb)
 
-itemRgb = '0,128,0' #Green
+#itemRgb = '0,128,0' #Green
 
 for line in rawFileNoHeader:
     line = line.rstrip().split("\t")
     if line[0].startswith("BRCA1"):
         varsToConvertToVcf.write("NM_007294.4:"+line[1]+"\n")
     elif line[0].startswith("BRCA2"):
         varsToConvertToVcf.write("NM_000059.4:"+line[1]+"\n")
     else:
         print("ERROR! Missing transcript")
 varsToConvertToVcf.close()
 rawFileNoHeader.close()
-outputVcfFile.close()
 
 bash("hgvsToVcf -noLeftShift hg38 /hive/data/inside/enigmaTracksData/varsToConvert.txt /hive/data/inside/enigmaTracksData/tempVcfFile")
 
 tempVcfFile = open('/hive/data/inside/enigmaTracksData/tempVcfFile','r')
 
 vcfVarCoords = {}
 for line in tempVcfFile:
     line = line.rstrip().split("\t")
     if line[0].startswith("#"):
         continue
     else:
         #Have the dic be the hgnsc as key (e.g. NM_007294.3:c.1081T>C) with a list of chr + vcfLocation
         #Also subtracting 1 to make a chr chromStart chromEnd format
         vcfVarCoords[line[2]] = [line[0],str(int(line[1])-1),line[1]]