6ec399788beeb064f90f425e1b99b5635d85699a
rhead
  Tue May 8 19:36:29 2012 -0700
Moved two functions from qaUtils to qaGbTracks, and got rid of a duplicated function from qaUtils.
diff --git src/utils/qa/qaGbTracks src/utils/qa/qaGbTracks
index 4c2e773..4a7e1a4 100755
--- src/utils/qa/qaGbTracks
+++ src/utils/qa/qaGbTracks
@@ -23,30 +23,41 @@
   genePredCheck
   pslCheck
   featureBits
   (a version of) countPerChrom
 
   creates 3 files:  outFile.summary, outFile.log, outFile.chrom
         """)
     parser.add_argument('db', help='the database to check')
     parser.add_argument('-s, --single', help ='tableList is the name of a single table',
                         action="store_true", dest="single")
     parser.add_argument('tableList', help=
                         'a file listing the tables to check, or the name of a single table')
     parser.add_argument('outFile', help='base name to give results files')
     return parser.parse_args()
 
+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, tables):
+    """Raises an exception if any table in the tables list does not exist in the database."""
+    for name in tables:
+        if not tableExists(db, name):
+            raise Exception("Table " + name + " in " + db + " does not exist")
+
 def getTableList():
     if args.single:
         return [args.tableList]
     else:
         with open(args.tableList, "r") as f:
             raw = f.readlines()
         return [name.strip() for name in raw]
 
 delimiterLine = "==============================================="
 def runTests():
     """Runs validate() and statistics() methods on each table. Writes log output."""
     reporter.writeTimestamp()
     reporter.writeBlankLine()
     for table in tableList:
         reporter.writeLine(delimiterLine)
@@ -59,30 +70,30 @@
     reporter.writeTimestamp()
 
 def writeSummaryFile():
     sumFile.write(sumTable.tabSeparated())
 
 def runChromCounts():
     chromFile.write(time.asctime() + "\n")
     chromFile.write("Database: " + args.db + "\n\n")
     tableSet = set(tableList)
     output, tablecounts = tableCheck.countPerChrom(args.db, tableSet)
     for line in output:
         chromFile.write(line + "\n")
 
 args = parseCommandLine()
 tableList = getTableList()
-qaUtils.checkTablesExist(args.db, tableList)
+checkTablesExist(args.db, tableList)
 
 logFile = open(args.outFile + ".log", "w")
 chromFile = open(args.outFile + ".chroms", "w")
 sumFile = open(args.outFile + ".summary", "w")
 reporter = reporter.Reporter(logFile)
 sumTable = summary.SumTable()
 
 runTests()
 runChromCounts()
 writeSummaryFile()
 
 logFile.close()
 sumFile.close()
 chromFile.close()