src/utils/qa/qaEncodeTracks.csh 1.7

Index: src/utils/qa/qaEncodeTracks.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/qaEncodeTracks.csh,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/utils/qa/qaEncodeTracks.csh	28 Jan 2010 01:27:16 -0000	1.6
+++ src/utils/qa/qaEncodeTracks.csh	4 Feb 2010 20:22:37 -0000	1.7
@@ -1,153 +1,153 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 ###############################################
 # 
 #  03-05-2009
 #  Ann Zweig
 #
 #  Runs through the usual checks for ENCODE
 #  tables.
 # 
 ###############################################
 
 set db=''
 set tableList=''
 set maxShortLabel='16'
 set maxLongLabel='80'
 
 if ($#argv != 2 ) then
   echo
   echo " Runs test suite for ENCODE tracks"
   echo " (it's best to direct output and errors to a file: '>&')"
   echo " In general, this script only prints output if there are problems" 
   echo
   echo "    usage: db tableList"
   echo
   exit 1
 else
   set db=$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
 
 # Takes too long to run (commented out for now):
 # featureBits for all tables
 #echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 #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 "*** check for tableDescription entry for all tables ***"
 echo "(Only prints tablename if there is NO entry in tableDescription table)"
 foreach table ( $tables )
  set num=`hgsql -Ne "select count(*) from tableDescriptions where tableName = '$table'" $db`
  if ( 0 == $num ) then
   echo "\nERROR: no description for $table"
  endif
 end
 
 # no underscores in table names
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 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 "_"
 
 # check that positional tables are sorted for all tables
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** check that positional tables are sorted ***"
 echo "(Only prints if the table is NOT sorted)"
 foreach table ( $tables )
  positionalTblCheck $db $table
 end
 
 # check table index for each table
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** Check table INDEX ***"
-echo "(Only prints the INDEX if there are less than two indices."
+echo "(Only prints the INDEX if there are fewer than two indices."
 echo "Presumably, these two will include bin and something else."
 echo "Note that bbi tables will have no index.)"
 foreach table ( $tables )
  set num=`hgsql -N -e "SHOW INDEX FROM $table" $db | wc -l`
  if ( $num < 2 ) then
-  echo "ERROR: $table has less than 2 indices"
+  echo "ERROR: $table has fewer than 2 indices"
  endif 
 end
 
 # checkTableCoords for each table (instead of checkOffend.csh)
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** checkTableCoords for each table ***"
 echo "(Only prints if there are coords off the end of a chrom)"
 foreach table ( $tables )
  checkTableCoords $db $table
 end
 
 # check the length of the shortLabel for each track
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** MAX length of shortLabel should be 16 ***"
 echo "(Only prints if shortLabel is greater than 16 characters, or if"
 echo "it can't find a shortLabel at all)"
 foreach table ( $tables )
  set num=`cat ~/trackDb/human/hg18/trackDb.wgEncode.ra | grep -A10 "track $table" \
   | grep -m 1 shortLabel \
   | sed -e 's/shortLabel //' | sed -e 's/^ *//' | sed -e 's/.$//' | wc -m`
  if ( $maxShortLabel < $num || 0 == $num ) then
   if ( 0 == $num ) then
    echo "ERROR: can't find a shortLabel for $table"
   else
    echo "ERROR: $table shortLabel is $num characters"
   endif
  endif
 end
 
 # check the length of the longLabel for each track
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** MAX length of longLabel should be 80 ***"
 echo "(Only prints if longLabel is greater than 80 characters, or if"
 echo "it can't find a longLabel at all)"
 foreach table ( $tables )
  set num=`cat ~/trackDb/human/hg18/trackDb.wgEncode.ra | grep -A10 "track $table" \
   | grep -m 1 longLabel \
   | sed -e 's/longLabel //' | sed -e 's/^ *//' | sed -e 's/.$//' | wc -m`
  if ( $maxLongLabel < $num || 0 == $num ) then
   if ( 0 == $num ) then
    echo "ERROR: can't find a longLabel for $table"
   else
    echo "ERROR: $table longLabel is $num characters"
   endif
  endif
 end
 
 # countPerChrom for all tables
 echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "*** countPerChrom for all tables ***"
 echo "(prints all counts here -- a useful way to look at this output is to"
 echo "grep for all 'chr4', for example)"
 foreach table ( $tables )
  echo ""
  echo "countPerChrom.csh $db $table"
  countPerChrom.csh $db $table
 end
 
 echo "\nthe end.\n"
 exit 0