564d7150acdd107cf31883feece7c11098d33740
max
  Wed Oct 30 21:58:37 2019 -0700
making chromFixer py3 compatible, refs #24407

diff --git src/utils/chromFixer/chromFixer src/utils/chromFixer/chromFixer
index f077e7f..bbf8216 100755
--- src/utils/chromFixer/chromFixer
+++ src/utils/chromFixer/chromFixer
@@ -1,148 +1,151 @@
 #!/usr/bin/env python
-import logging, optparse, gzip, StringIO
+import logging, optparse, gzip
 from sys import stdin, stdout, stderr, exit
-# support both py2 and py3
 try:
-    from urllib.request import urlopen
+    from urllib.request import urlopen # py2
 except ImportError:
-    from urllib2 import urlopen
+    from urllib2 import urlopen # py3
+try:
+    from cStringIO import StringIO # py2
+except ImportError:
+    from io import StringIO # py3
 
 # ==== functions =====
 def parseArgs():
     " setup logging, parse command line arguments and options. -h shows auto-generated help page "
     parser = optparse.OptionParser("""usage: %prog [options] filename - change NCBI or Ensembl chromosome names to UCSC names using the chromAlias table of the genome browser.
 
     Examples:
         %prog -i test.bed -o test.ucsc.bed -g hg19
         %prog -g mm10 --get
         %prog -i test2.bed -o test2.ucsc.bed -a mm10.chromAlias.tsv
         cat test.bed | %prog -a mm10.chromAlias.tsv > test.ucsc.edb
     """)
 
     parser.add_option("-g", "--genomeDb", dest="db", action="store", help="a UCSC assembly ID, like hg19, mm10 or similar. Not required if -a is used.")
     parser.add_option("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias table in tab-sep format.")
     parser.add_option("-i", "--in", dest="inFname", action="store", help="input filename, default: /dev/stdin")
     parser.add_option("-o", "--out", dest="outFname", action="store", help="output filename, default: /dev/stdout")
     parser.add_option("", "--get", dest="doDownload", action="store_true", help="download a chrom alias table from UCSC for --genomeDb into the current directory and exit")
     parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
     #parser.add_option("", "--test", dest="test", action="store_true", help="do something") 
     (options, args) = parser.parse_args()
 
     if options.db is None and options.aliasFname is None:
         parser.print_help()
         exit(1)
 
     if options.debug:
         logging.basicConfig(level=logging.DEBUG)
     else:
         logging.basicConfig(level=logging.INFO)
     return args, options
 
 # ----------- main --------------
 def splitLines(ifh):
     " yield (chromName, restOfLine) for all lines of ifh "
     sep = -1
     #if (sys.version_info > (3, 0)):
     lineNo = 0
     for line in ifh:
         if sep==-1:
             if "\t" in line:
                 sep = "\t"
             else:
                 sep = None # = split on any whitespace, consec. whitespc counts as one
         chrom, rest = line.split(sep, 1)
         lineNo += 1
         yield lineNo, sep, chrom, rest
 
 def parseAlias(fname):
     " parse tsv file with at least two columns, orig chrom name and new chrom name "
     toUcsc = {}
     for line in open(fname):
         if line.startswith("alias"):
             continue
         row = line.rstrip("\n").split("\t")
         toUcsc[row[0]] = row[1]
     return toUcsc
 
 def chromFixer(db, aliasFname, ifh, ofh):
     " convert the first column to UCSC-style chrom names "
     if aliasFname is None:
         toUcsc = aliasData[db]
     else:
         toUcsc = parseAlias(aliasFname)
 
     ucscChroms = set(toUcsc.values())
 
     mtSkipCount = 0
     for lineNo, sep, chrom, rest in splitLines(ifh):
         # just pass through any UCSC chrom names
         if chrom in ucscChroms:
             ucscChrom = chrom
         else:
             if db=="hg19" and (chrom=="MT" or chrom=="M"):
                 mtSkipCount += 1
                 continue
 
             ucscChrom = toUcsc.get(chrom)
             if ucscChrom is None:
                 logging.error("line %d: chrom name %s is not in chromAlias table" % (lineNo, repr(chrom)))
                 exit(1)
                 continue
 
         ofh.write(ucscChrom)
         ofh.write(sep)
         ofh.write(rest)
 
     if mtSkipCount!=0:
         stderr.write("%d features were skipped because they were located on the M or MT chromosome. hg19 includes an older version of the mitochondrial genome and these features cannot be mapped\n" % mtSkipCount)
 
 def patchScript(fnameStr, outFname):
     " read alias tables from fnameStr, put into this script and write patched script to outFname "
     aliasData = {}
     for fname in fnameStr.split(","):
         db = fname.split(".")[0]
         print("Reading alias table for %s: %s" % (db, fname))
         aliasData[db] = parseAlias(fname)
 
     myFname = __file__
     newScript = open(myFname).read().replace("#ALIASDATA#", "aliasData = "+repr(aliasData))
     open(outFname, "w").write(newScript)
     print("Patched script written to "+outFname)
     exit(0)
 
 def download(db):
     url = "http://hgdownload.soe.ucsc.edu/goldenPath/%s/database/chromAlias.txt.gz" % db
     gzData = urlopen(url).read()
     data = gzip.GzipFile(fileobj=StringIO.StringIO(gzData)).read()
     outFname = db+".chromAlias.tsv"
     open(outFname, "w").write(data)
     print("Wrote %s" % outFname)
     exit(0)
 
 def main():
     args, options = parseArgs()
 
     db = options.db
     aliasFname = options.aliasFname
     inFname = options.inFname
     outFname = options.outFname
 
     if db=="build":
         patchScript(aliasFname, outFname)
     if options.doDownload:
         download(db)
 
     if inFname is None:
         ifh = stdin
     else:
         ifh = open(inFname)
 
     if outFname is None:
         ofh = stdout
     else:
         ofh = open(outFname, "w")
 
     chromFixer(db, aliasFname, ifh, ofh)
 
 #ALIASDATA#
 main()