beec258cf09f6fb519a05e28a2ab17ca3fef4858
max
  Tue Mar 3 02:45:02 2020 -0800
another tiny docs change to chromToUcsc

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index 5051800..c0fe74d 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -6,36 +6,36 @@
 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 -g hg19 --get              # download the file hg19.chromAlias.tsv into current directory
         %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
 
     If you do not want to use the --get option to retrieve the mapping tables, you can also download the alias mapping
-    files yourself, e.g. for mm10: wget http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromAlias.txt.gz
+    files yourself, e.g. for mm10 with 'wget http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromAlias.txt.gz'
     """)
 
     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: