f5a1b930828e2737ee09d3dc71b3a0c9c2068452
max
  Wed Mar 27 08:21:03 2024 -0700
otto job for decipher failed, otto email

diff --git src/hg/utils/otto/decipher/processDecipher.py src/hg/utils/otto/decipher/processDecipher.py
index 9bf61ca..7479478 100755
--- src/hg/utils/otto/decipher/processDecipher.py
+++ src/hg/utils/otto/decipher/processDecipher.py
@@ -70,31 +70,31 @@
     if len(sys.argv) != 6:
         print ("Usage: makeUcscBed.py <input file> <genefile> <cnv output file> <snv output file> <snv raw output file>")
         sys.exit(0)
 
     cnvOutput = open(sys.argv[3], "w")
     snvOutput = open(sys.argv[4], "w")
     snvRawOutput = open(sys.argv[5], "w")
 
     geneFields = namedtuple("geneFields", ["chrom", "chromStart", "chromEnd", "name"])
     geneList = []
     with open(sys.argv[2]) as geneFile:
         for line in geneFile:
             fields = line.strip('\n').split('\t')
             geneList.append(geneFields(chrom=fields[0],chromStart=int(fields[1]),chromEnd=int(fields[2]),name=fields[3]))
 
-    with open(sys.argv[1], "r") as inputFile:
+    with open(sys.argv[1], "r", encoding="utf8") as inputFile:
         header = inputFile.readline()
         for line in inputFile:
             fields = line.strip('\n').split('\t')
             parsedJson = json.loads(fields[13])
 
             varType = parsedJson["variant_type"];
             if (varType == "SNV") :
                 # Make the basic table file
                 result = "\t".join(fields[:4])
                 print (result, file=snvOutput)
 
                 # Make the "raw" data file with more fields
                 # format: id, chrom, start, end, ref, alt, transcript, gene, genotype, inheritance, pathgenicity,
                     # contribution, phenotypes
                 fields[0] = fields[0].replace("chr", "")  # strip off initial "chr" for these names