85c51face300add10b745269401ffbdd632fe750
max
  Mon Nov 18 05:18:46 2019 -0800
fixing chromToUcsc, once more, the download --get example didn't work anymore, refs #24407

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index 2dacbd0..4a699e0 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -1,139 +1,139 @@
 #!/usr/bin/env python
 import logging, optparse, gzip
 from sys import stdin, stdout, stderr, exit, modules
 try:
     from urllib.request import urlopen # py2
 except ImportError:
     from urllib2 import urlopen # py3
 try:
     from cStringIO import StringIO # py2
 except ImportError:
     from io import BytesIO # 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 -g hg19 --get
         %prog -i test2.bed -o test2.ucsc.bed -a hg19.chromAlias.tsv -g hg19
         cat test.bed | %prog -a mm10.chromAlias.tsv > test.ucsc.bed
     """)
 
     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("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias table in tab-sep format. The alias tables for hg19 or hg38 are hardcoded in the script, they do not require a chromAlias table. Use the -g option for those.")
     parser.add_option("-g", "--genomeDb", dest="db", action="store", help="a UCSC assembly ID, like hg19. Not required. Activates assembly-specific warning messages, only for hg19 right now.")
     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("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
     (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 chromToUcsc(db, aliasFname, ifh, ofh):
     " convert the first column to UCSC-style chrom names "
     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 yet.\n" % mtSkipCount)
 
 def download(db):
     url = "http://hgdownload.soe.ucsc.edu/goldenPath/%s/database/chromAlias.txt.gz" % db
     gzData = urlopen(url).read()
 
     if 'cStringIO' in modules:
         data = StringIO(gzData)
     else:
         data = BytesIO(gzData)
     
     data = gzip.GzipFile(fileobj=data).read().decode()
     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 options.doDownload:
+        download(db)
+
     if aliasFname is None:
         logging.error("You need to provide an alias table with the -a option")
         exit(1)
 
-    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")
 
     chromToUcsc(db, aliasFname, ifh, ofh)
 
 main()