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 @@ -56,32 +56,32 @@ 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):