0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd
max
  Fri Sep 20 13:18:01 2024 -0700
Revert "more features to hubtools: search in both parent and subdirs, better docs"

This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.

diff --git src/hg/makeDb/cadd/caddToWig.py src/hg/makeDb/cadd/caddToWig.py
index 99bf4a1..0eb21ab 100644
--- src/hg/makeDb/cadd/caddToWig.py
+++ src/hg/makeDb/cadd/caddToWig.py
@@ -1,64 +1,63 @@
-import sys
 import subprocess
 
 def inputLineChunk():
     " yield all values at consecutive positions as a tuple (chrom, pos, list of (nucl, phred value)) "
     ## CADD GRCh37-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2019. All rights reserved.
     #Chrom  Pos     Ref     Alt     RawScore        PHRED
     #1       10001   T       A       0.088260        4.066
     values = []
     firstChrom = None
     firstPos = None
     lastChrom = None
     lastPos = None
 
     #for line in gzip.open("whole_genome_SNVs.tsv.gz"):
-    for line in subprocess.Popen(['zcat', sys.argv[1]], stdout=subprocess.PIPE, encoding="ascii").stdout:
+    for line in subprocess.Popen(['zcat', "whole_genome_SNVs.tsv.gz"], stdout=subprocess.PIPE, encoding="ascii").stdout:
         if line.startswith("#"):
             continue
         row = line.rstrip("\n").split("\t")
         chrom, pos, ref, alt, raw, phred = row
         chrom = "chr"+chrom
         pos = int(row[1])
         phred = float(phred)
 
         if firstPos is None:
             firstChrom = chrom
             firstPos = pos
 
         if chrom!=lastChrom or pos-lastPos > 1 and firstChrom is not None:
             yield firstChrom, firstPos, values
             firstPos, firstChrom = None, None
             values = []
 
         if pos != lastPos:
             values.append([0.0,0.0,0.0,0.0])
         nuclIdx = "ACGT".find(alt)
         values[-1][nuclIdx] = phred
 
         lastPos = pos
         lastChrom = chrom
     # last line of file
     yield firstChrom, firstPos, values
 
 outFhs = {
         "A" : open("a.wig", "w"),
         "C" : open("c.wig", "w"),
         "T" : open("t.wig", "w"),
         "G" : open("g.wig", "w")
         }
 
 for chrom, pos, nuclValues in inputLineChunk():
     if len(nuclValues)==0:
         continue
 
     for ofh in outFhs.values():
         ofh.write("fixedStep chrom=%s span=1 step=1 start=%d\n" % (chrom, pos))
 
     for nuclVals in nuclValues:
         for nucIdx in (0,1,2,3):
             alt = "ACGT"[nucIdx]
             ofh = outFhs[alt]
             phred = nuclVals[nucIdx]
             ofh.write(str(phred))
             ofh.write("\n")