src/utils/qa/qaEncodeTracks.csh 1.2

Index: src/utils/qa/qaEncodeTracks.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/qaEncodeTracks.csh,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/utils/qa/qaEncodeTracks.csh	28 Jul 2009 16:04:10 -0000	1.1
+++ src/utils/qa/qaEncodeTracks.csh	28 Jul 2009 16:13:01 -0000	1.2
@@ -1,137 +1,138 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 ###############################################
 # 
 #  03-05-2009
 #  Ann Zweig
 #
 #  Runs through the usual checks for ENCODE
 #  tables.
 # 
 ###############################################
 
 set db=''
 set tableList=''
 
 if ($#argv != 2 ) then
   echo
   echo "  runs test suite for ENCODE tracks"
   echo "  (it's best to direct output and errors to a file: '>&')"
   echo
   echo "    usage: db tableList"
   echo
   exit 1
 else
   set db=$argv[1]
   set tableList=$argv[2]
 endif
 
 # run only from hgwdev
 if ( "$HOST" != "hgwdev" ) then
   echo "\nERROR: you must run this script on hgwdev!\n"
   exit 1
 endif
 
 # check to see if it is a single tableName or a tableList
 file $tableList | egrep "ASCII text" > /dev/null
 if (! $status) then
  set tables=`cat $tableList`
 else
  set tables=$tableList
 endif
 
 
 # featureBits for all tables
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** featureBits for all tables ***"
 foreach table ( $tables )
  echo ""
  echo "featureBits -countGaps $db $table"
  nice featureBits -countGaps $db $table
  echo "featureBits -countGaps $db $table gap"
  nice featureBits -countGaps $db $table gap
 end
 
 # check for table descriptions for all tables
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** check for tableDescription entry for all tables ***"
 echo "Is there an entry in the tableDescriptions table for each"
 echo "table? (1 == yes, 0 == no)"
 foreach table ( $tables )
  echo ""
  echo "Table: $table"
  hgsql -Ne "select count(*) from tableDescriptions where tableName = '$table'" $db
 end
 
 # no underscores in table names
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** make sure there are no underscores in table names ***"
 echo "If there's output here, you have one or more tables with "_":"
 echo $tables | grep "_"
 echo ""
 
 # check that positional tables are sorted for all tables
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** check that positional tables are sorted ***"
 echo "(No output means table is sorted)"
 foreach table ( $tables )
  echo ""
  echo "positionalTblCheck $db $table"
  positionalTblCheck $db $table
 end
 
 # check table index for each table
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** Check table INDEX ***"
 foreach table ( $tables )
  echo ""
  echo ""
  hgsql -e "SHOW INDEX FROM $table" $db
 end
 
 # checkTableCoords for each table (instead of checkOffend.csh)
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** checkTableCoords for each table ***"
 foreach table ( $tables )
  checkTableCoords $db $table
 end
 echo "\n(Nothing will be printed if all are okay.)"
 
 # check the length of the shortLabel for each track
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** MAX length of shortLabel should be 16 ***"
 foreach table ( $tables )
  echo "Table: $table"
  cat ~/trackDb/human/hg18/trackDb.wgEncode.ra | grep -A10 "track $table" | grep shortLabel \
   | sed -e 's/shortLabel //' | sed -e 's/^ *//' | sed -e 's/.$//' | wc -m
 end
 
 # check the length of the longLabel for each track
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** MAX length of longLabel should be 80 ***"
 foreach table ( $tables )
  echo "Table: $table"
  cat ~/trackDb/human/hg18/trackDb.wgEncode.ra | grep -A10 "track $table" | grep longLabel \
   | sed -e 's/longLabel //' | sed -e 's/^ *//' | sed -e 's/.$//' | wc -m
 end
 
 # countPerChrom for all tables
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** countPerChrom for all tables ***"
 foreach table ( $tables )
  echo ""
  echo "countPerChrom.csh $db $table"
  countPerChrom.csh $db $table
 end
 
 echo "\nthe end.\n"
 exit 0