50c0049649c7268bd12ab0689cda7f8261b46a63
chmalee
  Mon May 6 16:11:42 2019 -0700
DGV Gold track mostly ready for QA, refs #23371

diff --git src/hg/utils/automation/translateDgvGold.py src/hg/utils/automation/translateDgvGold.py
index 9e72afc..c412ff3 100755
--- src/hg/utils/automation/translateDgvGold.py
+++ src/hg/utils/automation/translateDgvGold.py
@@ -1,114 +1,114 @@
 #!/bin/env python
 """
 Parses the Gold-standard copy number variants GFF from DGV and writes
 a tab separated bed 12 with extra fields to stdout.
 
 Example:
 ./translateDgvGold.py input.gff | sort -k1,1 -k2,2n | uniq > output.bed12
 """
 
 import sys
 
 header = "chrom\tchromStart\tchromEnd\tname\tscore\tstrand\tthickStart\tthickEnd\t" \
     "itemRgb\tblockCount\tblockSizes\tblockStarts"
 
 # gain blue, loss red
 colors = {"Gain": "0,0,200", "Loss": "200,0,0"}
 
 def parseExtraInfo(extraInfoList, doHeader=False):
     """ Parses the 9th field of the DGV Gold GFF and optionally assigns the header."""
     info = []
     extraHeader = []
     for x in extraInfoList:
         s = x.split("=")
         if doHeader:
             extraHeader.append(s[0])
         info.append(s[1])
 
     name = info[1]
     subType = info[3]
     outerStart = info[4]
     innerStart = info[5]
     innerEnd = info[6]
     outerEnd = info[7]
 
     # delete fields that are gonna be in the normal bed fields
     info.remove(name)
     info.remove(outerStart)
     info.remove(innerStart)
     info.remove(innerEnd)
     info.remove(outerEnd)
     extraString = "\t".join(info)
 
     if doHeader:
         global header
         extraHeader.remove("Name")
         extraHeader.remove("outer_start")
         extraHeader.remove("inner_start")
         extraHeader.remove("inner_end")
         extraHeader.remove("outer_end")
         header += "\t" + "\t".join(extraHeader)
 
     return name, subType, outerStart, innerStart, innerEnd, outerEnd, extraString
 
 ### main ###
 
-if len(sys.argv) != 1:
+if len(sys.argv) != 2:
     print("Usage: translateDgvGold.py input.gff | sort -k1,1 -k2,2n | uniq > out.bed12\n"\
             "\nWrites a bed12 to stdout.\n")
     sys.exit(1)
 
 doHeader = True
 
 for line in open(sys.argv[1]):
     gffFields = line.strip().split("\t")
     extraInfo = gffFields[8].split(";")
     chrom = gffFields[0]
     name, subType, outerStart, innerStart, innerEnd, chromEnd, extraString = parseExtraInfo(extraInfo, doHeader)
     if subType not in colors:
         sys.exit("CNV subtype: %s not recognized.\n" % subType)
 
     chromStart = str(int(outerStart) - 1)
 
     # one block
     if innerStart == outerStart and innerEnd == chromEnd:
         blockCount = "1"
         blockSizes = str(int(chromEnd) - int(chromStart))
         blockStarts = "0"
     # no left intron 
     elif outerStart == innerStart:
         blockCount = "2"
         blockStarts = "0," + str(int(chromEnd) - int(chromStart) - 1)
         blockSizes = str(int(innerEnd) - int(chromStart)) + ",1"
     # no right intron
     elif innerEnd == chromEnd:
         blockCount = "2"
         blockStarts = "0," + str(int(innerEnd) - (int(innerEnd) - int(innerStart)) - int(chromStart))
         blockSizes = "1," + str(int(innerEnd) - int(innerStart))
     # two introns
     else:
         blockCount = "3"
         blockSizes = "1,"+ str(int(innerEnd) - int(innerStart))+",1"
         blockStarts = "0," + \
             str(int(innerStart)-int(chromStart)) + \
             ","+str(int(chromEnd)-int(chromStart)-1)
 
     bedLine = [chrom,
         chromStart,
         chromEnd,
         name,
         "0",
         ".",
         chromEnd,
         chromEnd,
         colors[subType],
         blockCount,
         blockSizes,
         blockStarts,
         extraString]
 
     if doHeader:
         print("#" + header)
 
     print("\t".join(bedLine))
     doHeader = False