7a8fdcbb9b6b28ffdeee0a1da8bb83a3c68c7ed8
max
  Fri Jun 4 06:03:33 2021 -0700
fixing up makedocs and track docs for revel track, refs #27142

diff --git src/hg/makeDb/revel/revelToWig-hg38.py src/hg/makeDb/revel/revelToWig-hg38.py
index 1e2036f..8dcffc8 100644
--- src/hg/makeDb/revel/revelToWig-hg38.py
+++ src/hg/makeDb/revel/revelToWig-hg38.py
@@ -1,115 +1,115 @@
 import subprocess, sys
 from collections import defaultdict
 #from array import array
 import numpy as np
 
 # based on revelToWig.py in kent/src/hg/makeDb/scripts/revel/
 # three arguments: chrom.sizes, input filename and db (one of: hg19, hg38)
 
 def parseChromSizes(chromSizesFname):
     chromSizes = {}
     for line in open(chromSizesFname):
         chrom, size = line.strip().split()
         size = int(size)
         chromSizes[chrom] = size
     return chromSizes
 
 def initValues(chromSizes, chrom):
     print('init arrays for chrom %s' % chrom)
     arrs = []
     for n in range(0, 4):
         #a = array('f', chromSizes[chrom]*[-1])
         a = np.full(chromSizes[chrom], -1, dtype=float)
         arrs.append(a)
     print('arrays done')
     return arrs
 
 def inputLineChunk(fname, chromSizes):
     " read all values for one chrom and return as four arrays, -1 means 'no value'"
     # chr,hg19_pos,grch38_pos,ref,alt,aaref,aaalt,REVEL
     values = []
 
     if fname.endswith(".gz"):
         ifh = subprocess.Popen(['zcat', fname], stdout=subprocess.PIPE, encoding="ascii").stdout
     else:
         ifh = open(fname)
 
     chromValues = initValues(chromSizes, "chr1")
     lastChrom = "1"
     for line in ifh:
         if line.startswith("chr"):
             continue
         row = line.rstrip("\n").split(",")[:8]
 
         chrom, hg19Pos, hg38Pos, ref, alt, aaRef, aaAlt, revel = row
         pos = hg38Pos
         if pos==".":
             continue
 
         pos = int(pos)-1 # wiggle ascii is 1-based AAARRGH!!
         # but I keep everythin 0 based internally
         # the file has duplicate values in the hg38 column, but for different hg19 positions!
         revel = float(revel)
 
         if chrom != lastChrom and lastChrom!=None:
             yield lastChrom, chromValues
             lastChrom = chrom
             chromValues = initValues(chromSizes, "chr"+chrom)
 
         nuclIdx = "ACGT".find(alt)
         chromValues[nuclIdx][pos] = revel
 
     # last line of file
     yield chrom, chromValues
 
 chromSizesFname = sys.argv[1]
 fname = sys.argv[2]
 
 outFhs = {
         0 : open("a.wig", "w"),
         1 : open("c.wig", "w"),
-        2 : open("t.wig", "w"),
-        3 : open("g.wig", "w")
+        2 : open("g.wig", "w"),
+        3 : open("t.wig", "w")
         }
 
 chromSizes = parseChromSizes(chromSizesFname)
 
 for chrom, nuclValues in inputLineChunk(fname, chromSizes):
     if len(nuclValues)==0:
         continue
 
     # need to find positions that have no values at all:
     # so we can distinguish: "has no value" (not covered) with "is reference"
     # (value=0)
     arrSum = np.sum(nuclValues, axis=0)
     # positions without any data have now arrSum[i]==-4
 
     for nucIdx in (0,1,2,3):
         arr = nuclValues[nucIdx]
         ofh = outFhs[nucIdx]
         lastVal = arr[0]
         stretch = []
         stretchStart = 0
         for i in range(0, arr.size):
             val = arr[i]
             hasData = (arrSum[i]!=-4)
 
             if val==-1 and hasData:
                 if len(stretch)==0:
                     stretchStart = i
                 stretch.append(0)
             elif val!=-1:
                 if len(stretch)==0:
                     stretchStart = i
                 stretch.append(val)
             else:
                 # there is no data at all at this position, so flush the block
                 if len(stretch)!=0:
                     ofh.write("fixedStep chrom=chr%s span=1 step=1 start=%d\n" % (chrom, stretchStart+1))
                     for revel in stretch:
                         ofh.write(str(revel))
                         ofh.write("\n")
                     ofh.write("\n")
                 stretchStart = None
                 stretch = []