2ae4d94adb7cb66f48c5c6f2b686cd9db29fca16
max
  Fri Sep 20 05:50:51 2019 -0700
removing mastermind files, now they are ottomatic

diff --git src/hg/makeDb/mastermind/mastermindToBed.py src/hg/makeDb/mastermind/mastermindToBed.py
deleted file mode 100644
index e7f1aaa..0000000
--- src/hg/makeDb/mastermind/mastermindToBed.py
+++ /dev/null
@@ -1,61 +0,0 @@
-# convert mastermind .csv file to .bed with extra fields
-# arguments: $1 = mastermind csv file
-# output goes to mastermind.bed
-import re, sys, csv
-
-csv.field_size_limit(sys.maxsize)
-
-ncbiToUcsc = {}
-
-for line in open("chromAlias.tab"):
-    row = line.rstrip("\n").split("\t")
-    ncbiToUcsc[row[0]] = row[1]
-
-ofh = open("mastermind.bed", "w")
-
-prefixRe = re.compile(r'NC_[0-9]*.[0-9]*:g.[0-9_]*')
-
-fname = sys.argv[1]
-reader = csv.reader(open(fname))
-
-for row in reader:
-    #CHROM,POS,ID,REF,ALT,QUAL,FILTER,GENE,HGVSG,MMCNT1,MMCNT2,MMCNT3,MMID3,MMURI3
-    if row[0].startswith("CHROM"):
-        continue
-    ncbiChrom, pos, _, ref, alt, _, _, gene, hgvsg, mmcnt1, mmcnt2, mmcnt3, mmid3, mmuri3 = row
-    mmid3s = mmid3.split(",")
-    mmuri3s = mmuri3.split(",")
-
-    chrom = ncbiToUcsc[ncbiChrom]
-    start = int(pos)-1
-    end = start+len(ref)
-    name = prefixRe.sub("", hgvsg)
-    if len(name)>17:
-        name = name[:14]+"..."
-    if len(mmid3s)==1:
-        mouseOver = mmid3+" - %s/%s/%s" % (mmcnt1, mmcnt2, mmcnt3)
-    else:
-        mouseOver = mmid3+" on %d transcripts - %s/%s/%s" % (len(mmid3s), mmcnt1, mmcnt2, mmcnt3)
-
-    score = "0"
-    strand = "."
-    # values copied from knownGene.html
-    itemRgb = "130,130,210" # light blue by default: mmcnt3==1
-    if int(mmcnt3)>1: # medium-blue if mmcnt3 >=2
-        itemRgb = "50,80,160"
-    if int(mmcnt1)!=0: # dark-blue if exact cDNA match
-        itemRgb = "12,12,120"
-
-    urlSuffix = mmuri3s[0].replace("https://mastermind.genomenon.com/detail?disease=all%20diseases&", "")
-    assert(urlSuffix!=mmuri3)
-
-    url = urlSuffix+"|"+mmid3
-    outRow = [chrom, str(start), str(end), name, score, strand, str(start), str(end), itemRgb, url, gene, mmcnt1, mmcnt2, mmcnt3, mouseOver]
-    ofh.write("\t".join(outRow))
-    ofh.write("\n")
-
-print("Wrote %s" % ofh.name)
-
-
-
-