4a819ccfe7f5074c2295daacd838731fe59534fb
max
  Tue Sep 17 02:16:07 2019 -0700
new avada track, refs #24156

diff --git src/hg/makeDb/avada/toBed.py src/hg/makeDb/avada/toBed.py
new file mode 100644
index 0000000..1cb90fd
--- /dev/null
+++ src/hg/makeDb/avada/toBed.py
@@ -0,0 +1,37 @@
+# convert avada to bed
+import gzip
+for line in gzip.open("avada_v1.00_2016.vcf.gz", "rt"):
+    if line.startswith("#"):
+        continue
+    row = line.rstrip("\n").split("\t")
+    # ['1', '45797228', '.', 'C', 'T', '.', '.', 'PMID=23361220;GENE_SYMBOL=MUTYH;ENSEMBL_ID=ENSG00000132781;ENTREZ_ID=4595;REFSEQ_ID=NM_001128425.1;STRAND=-;ORIGINAL_VARIANT_STRING=c.1187G4A']
+    chrom, start, qual, ref, alt, dot1, dot2, otherStr = row
+    otherParts = otherStr.split(';')
+    annots = {}
+    for p in otherParts:
+        key, val = p.split("=")
+        annots[key] = val
+
+    # bed9
+    chrom = "chr"+chrom
+    start = int(start)
+    end = start+len(ref)
+    name = annots["ORIGINAL_VARIANT_STRING"]
+    score = "0"
+    strand = annots["STRAND"]
+    thickStart = start
+    thickEnd = end
+    itemRgb = "0"
+    # extraFields:
+    pmid = annots["PMID"]
+    variant = name # easier for users, so variant is together with gene / paper
+    geneSym = annots["GENE_SYMBOL"]
+    ensId = annots["ENSEMBL_ID"]
+    entrez = annots["ENTREZ_ID"]
+    refseq = annots["REFSEQ_ID"]
+    
+    bed = [chrom, str(start), str(end), name, score, strand, str(thickStart), str(thickEnd), itemRgb, \
+            pmid, geneSym, variant, ensId, entrez, refseq]
+
+    print("\t".join(bed))
+