c8cf0851df29747fc97ace2912d452ac4d815b45
chmalee
  Mon Aug 10 06:24:35 2020 -0700
Fixing some problems in clinGenDosage otto job after code review feedback, refs #25996

diff --git src/hg/utils/otto/clinGen/processClinGenDosage.py src/hg/utils/otto/clinGen/processClinGenDosage.py
index fe22d0f..be84d97 100755
--- src/hg/utils/otto/clinGen/processClinGenDosage.py
+++ src/hg/utils/otto/clinGen/processClinGenDosage.py
@@ -53,37 +53,41 @@
         print("Only one of regionFile or geneFile can be stdin")
         sys.exit(1)
     return args
 
 def getColor(bed):
     """Return the shade of the item according to ClinGen rules. Red or blue for score 3, everything
         else gray."""
     retColors = {"haplo": "128,128,128", "triplo": "128,128,128"}
     if bed["Haploinsufficiency Score"] == "3": retColors["haplo"] = "255,0,0"
     if bed["Triplosensitivity Score"] == "3": retColors["triplo"] = "0,0,255"
     return retColors
 
 def getMouseover(bed):
     """Return the mouseOver strings for this bed record."""
     hapScore = bed["Haploinsufficiency Score"]
+    if not hapScore or hapScore == "Not yet evaluated":
+        hapScore = -1
     tripScore = bed["Triplosensitivity Score"]
+    if not tripScore or tripScore == "Not yet evaluated":
+        tripScore = -1
     ret = {"haplo": "", "triplo": ""}
     mouseOver = "Gene/ISCA ID: %s" % bed["name"]
     ret["triplo"] = mouseOver + ", Triplosensitivity: "
-    ret["triplo"] += "%s - %s" % (tripScore, scoreExplanation[int(tripScore)] if tripScore and tripScore != "Not yet evaluated" else -1)
+    ret["triplo"] += "%s - %s" % (tripScore, scoreExplanation[int(tripScore)])
     ret["haplo"] = mouseOver + ", Haploinsufficiency: "
-    ret["haplo"] += "%s - %s" % (hapScore, scoreExplanation[int(hapScore)] if hapScore and hapScore != "Not yet evaluated" else -1)
+    ret["haplo"] += "%s - %s" % (hapScore, scoreExplanation[int(hapScore)])
     return ret
 
 def parsePosition(posStr):
     """Turn a chr:start-stop string into bed chrom, chromStart, chromEnd"""
     try:
         colonDelim = posStr.split(":")
         chrom = colonDelim[0]
         dashDelim = colonDelim[1].split("-")
         start = int(dashDelim[0]) - 1
         end = int(dashDelim[1])
     except IndexError:
         sys.stderr.write("bad position string: %s\n" % posStr)
         sys.exit(1)
     return (chrom, start, end)
 
@@ -185,31 +189,33 @@
         triploBed += [bed[field] for field in triploFields] + [bed ["_mouseOver"]["triplo"]]
         print("\t".join(haploBed), file=haploFile)
         print("\t".join(triploBed), file=triploFile)
     haploFile.close()
     triploFile.close()
 
 def parseOmim(infh):
     with open(infh) as f:
         for line in f:
             omimId,phenotype = line.strip().split('\t')
             omimData[omimId] = phenotype
 
 def parseInFile(fname, fileType="gene"):
     if fname != "stdin":
         f = open(fname)
-    lineNumber = 1
+    else:
+        f = sys.stdin
+    lineNumber = 0
     for line in f:
         lineNumber += 1
         bizarreRecord = False
         if line.startswith("#"):
             continue
         l = line.strip("\n").split("\t")
         key = l[0] # geneSymbol or ISCA id
         extra = l[1:]
         if key in inData:   
             print("duplicate info for gene symbol: '%s'" % (geneSymbol))
             sys.exit(1)
         else:
             temp = {}
             fileFields = []
             if fileType == "gene":