bbd56c4fc8f1a411fcbbe33ef0a21b65fe230a6d
rhead
  Mon Sep 24 00:24:04 2012 -0700
Changed qaGbTracks so that it prints statistics about chromosome item counts to log file rather than the count of every chrom to a separate chrom file.  See redmine #9075.
diff --git src/utils/qa/qaGbTracks src/utils/qa/qaGbTracks
index 284aecc..839108a 100755
--- src/utils/qa/qaGbTracks
+++ src/utils/qa/qaGbTracks
@@ -1,97 +1,88 @@
 #!/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
-  (a version of) countPerChrom
+  item count per chromosome stats
 
-  creates 3 files:  outFile.summary, outFile.log, outFile.chrom
+  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 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(delimiterLine)
     reporter.writeLine("Tests complete:")
     reporter.writeTimestamp()
 
 def writeSummaryFile(sumTable, sumFile):
     sumFile.write(sumTable.tabSeparated())
 
-def runChromCounts(db, tableList, chromFile):
-    chromFile.write(time.asctime() + "\n")
-    chromFile.write("Database: " + db + "\n\n")
-    tableSet = set(tableList)
-    output, tablecounts = tableCheck.countPerChrom(db, tableSet)
-    for line in output:
-        chromFile.write(line + "\n")
-
 args = parseCommandLine()
 tableList = args.table
 db = args.db
 outFile = args.outFile
 checkTablesExist(db, tableList)
 
 logFile = open(outFile + ".log", "w")
-chromFile = open(outFile + ".chroms", "w")
 sumFile = open(outFile + ".summary", "w")
 reporter = reporter.Reporter(logFile)
 sumTable = summary.SumTable()
 
 runTests(db, tableList, reporter, sumTable)
-runChromCounts(db, tableList, chromFile)
 writeSummaryFile(sumTable, sumFile)
 
 logFile.close()
 sumFile.close()
-chromFile.close()