0e016ca51069bf70ea5c9e08d7ef2fa4dd81a838
max
  Wed Feb 10 06:11:16 2021 -0800
adding makedoc for cadd track, refs #18492

diff --git src/hg/makeDb/cadd/caddToBed.py src/hg/makeDb/cadd/caddToBed.py
new file mode 100644
index 0000000..d902ef4
--- /dev/null
+++ src/hg/makeDb/cadd/caddToBed.py
@@ -0,0 +1,36 @@
+import sys
+import subprocess
+## CADD GRCh38-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2020. All rights reserved.
+#Chrom  Pos     Ref     Alt     RawScore        PHRED
+#1       10061   T       TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC        0.199964        3.123
+#1       10067   T       TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC      0.225348        3.416
+#1       10108   C       CA      0.390514        5.321
+
+insFh = open("ins.bed", "w")
+delFh = open("del.bed", "w")
+
+inFname = sys.argv[1]
+for line in subprocess.Popen(['zcat', inFname], 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])-1
+    phred = float(phred)
+
+    if len(ref) < len(alt):
+        # insertion
+        insLen = len(alt)-1
+        name = str(insLen)
+        desc = "ins."+alt[1:]
+        ofh = insFh
+    else:
+        delLen = len(ref)-1
+        name = str(delLen)
+        desc = "del."+ref[1:]
+        ofh = delFh
+
+    bed = [chrom, str(pos), str(pos+1), name, str(round(phred)), ".", str(pos), str(pos+1), "0", desc, str(phred)]
+    ofh.write("\t".join(bed))
+    ofh.write("\n")