db09ffb4f2f00a9391334ce3e8b3cbe5fcc98cb5
max
  Tue Nov 22 03:50:26 2022 -0800
shorten arg for bigGuessDb tool, refs #30316

diff --git src/utils/bigGuessDb/bigGuessDb src/utils/bigGuessDb/bigGuessDb
index 731cd83..0edd832 100755
--- src/utils/bigGuessDb/bigGuessDb
+++ src/utils/bigGuessDb/bigGuessDb
@@ -7,31 +7,31 @@
 from collections import defaultdict
 from os.path import join, isfile, expanduser
 import os, gzip, subprocess
 
 # ==== functions =====
 def parseArgs():
     " setup logging, parse command line arguments and options. -h shows auto-generated help page "
     parser = optparse.OptionParser("usage: %prog [options] filename - given a bigBed or "\
             "bigWig file, " \
         "guess the assembly based on the chrom sizes")
 
     parser.add_option("-d", "--debug", dest="debug", action="store_true", \
         help="show debug messages")
     parser.add_option("", "--index", dest="index", action="store_true", \
         help="go /hive/data/genomes and build a file ~/.guessAssembly.txt with all chromSizes")
-    parser.add_option("-b", "--onlyBest", dest="onlyBest", action="store_true", \
+    parser.add_option("-b", "--best", dest="best", action="store_true", \
         help="only print a single string, the best matching assembly")
     (options, args) = parser.parse_args()
 
     if args==[] and not options.index:
         parser.print_help()
         exit(1)
 
     if options.debug:
         logging.basicConfig(level=logging.DEBUG)
         logging.getLogger().setLevel(logging.DEBUG)
     else:
         logging.basicConfig(level=logging.INFO)
         logging.getLogger().setLevel(logging.INFO)
 
     return args, options
@@ -144,21 +144,21 @@
 
 # ----------- main --------------
 def main():
     " entry point to script "
     args, options = parseArgs()
 
     indexFname = expanduser("~/.guessAssembly.txt.gz")
     if options.index:
         buildIndex("/hive/data/genomes", indexFname)
     else:
         inFname = args[0]
         fileSizes = bigWigSizes(inFname)
 
         sizeIndex = readSizeIndex(indexFname)
         hits = findBestDb(sizeIndex, fileSizes)
-        if options.onlyBest:
+        if options.best:
             print(hits[0][0])
         else:
             printAllMatches(hits)
 
 main()