36a49772a10673662471b7b1edc2e1744006a466
mspeir
  Wed Feb 15 09:48:59 2017 -0800
Tweaking usage message to mention runBits.csh. Adding main function to qaGbTracks. no redmine

diff --git src/utils/qa/qaGbTracks src/utils/qa/qaGbTracks
index e55b2bf..83869c1 100755
--- src/utils/qa/qaGbTracks
+++ src/utils/qa/qaGbTracks
@@ -1,95 +1,101 @@
 #!/usr/bin/env python2.7
 import sys
 import argparse
 import time
 
 from ucscGb.qa import qaUtils
 from ucscGb.qa.tables import factory
 from ucscGb.qa.tables import reporter
 from ucscGb.qa.tables import summary
 from ucscGb.qa.encode import tableCheck
 
 def parseCommandLine():
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
         description='Validates tables and records table statistics',
         epilog="""
 The following tests are run:
   checks for underscores in table names
   checks for the existence of table descriptions
   checks shortLabel and longLabel length
   positionalTblCheck
   checkTblCoords
   genePredCheck
   pslCheck
 
 The following statistics are recorded: 
-  featureBits
+  featureBits (via runBits.csh)
+  Overlap with gaps (including unbridged via runBits.csh)
   item count per chromosome stats
 
   creates 2 files:  outFile.summary, outFile.log
         """)
     parser.add_argument('db', help='the database to check')
     parser.add_argument('-f', dest='tableFile', nargs=1, type=argparse.FileType('r'),
                         help='a file listing tables to check (separated by spaces or newlines)')
     parser.add_argument('table', help ='the name of a table to check', nargs='*')
     parser.add_argument('outFile', help='base name to give results files')
     args = parser.parse_args()
     if args.tableFile:
         # add any additional tables in the table file to the table list
         args.table.extend((args.tableFile[0].read()).split())
         args.tableFile[0].close()
     return args
 
 def checkTablesReceived(tableList, outFile):
     """Raises an exception if the tableList is empty. (Necessary because both ways of specifying
     tables are optional.)"""
     if not tableList:
         raise Exception("Received outFile name '" + outFile + "', but no tables were specified.")
 
 def tableExists(db, table):
     """True if the table exists in the given database."""
     sqlResult = qaUtils.callHgsql(db, "show tables like '" + table + "'")
     return sqlResult.strip() == table
 
 def checkTablesExist(db, tableList):
     """Raises an exception if any table in the tables list does not exist in the database."""
     for name in tableList:
         if not tableExists(db, name):
             raise Exception("Table " + name + " in " + db + " does not exist")
 
 def runTests(db, tableList, reporter, sumTable):
     """Runs validate() and statistics() methods on each table. Writes log output."""
     delimiterLine = "==============================================="
     reporter.writeTimestamp()
     reporter.writeBlankLine()
     for table in tableList:
         reporter.writeLine(delimiterLine)
         reporter.writeLine(db + "." + table +":\n")
         table = factory.tableQaFactory(db, table, reporter, sumTable)
         table.validate()
         reporter.writeBlankLine()
         table.statistics()
     reporter.writeLine("Tests complete:")
     reporter.writeTimestamp()
 
 def writeSummaryFile(sumTable, sumFile):
     sumFile.write(sumTable.tabSeparated())
 
+def main():
+    """Main function of qaGbTracks. Runs all of the other functions of the program."""
     args = parseCommandLine()
     tableList = args.table
     db = args.db
     outFile = args.outFile
     checkTablesReceived(tableList, outFile)
     checkTablesExist(db, tableList)
 
     logFile = open(outFile + ".log", "w")
     sumFile = open(outFile + ".summary", "w")
-reporter = reporter.Reporter(logFile)
+    myReporter = reporter.Reporter(logFile)
     sumTable = summary.SumTable()
 
-runTests(db, tableList, reporter, sumTable)
+    runTests(db, tableList, myReporter, sumTable)
     writeSummaryFile(sumTable, sumFile)
 
     logFile.close()
     sumFile.close()
+
+if __name__ == "__main__":
+    main()