src/utils/qa/checkEncodeRegions.csh 1.7

Index: src/utils/qa/checkEncodeRegions.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/checkEncodeRegions.csh,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/utils/qa/checkEncodeRegions.csh	1 Nov 2007 21:31:43 -0000	1.6
+++ src/utils/qa/checkEncodeRegions.csh	11 Apr 2009 00:37:01 -0000	1.7
@@ -1,125 +1,126 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 ################################
 #
 # 07-26-2007
 # Ann Zweig
 #
 # This script is to be used on ENCODE tables.  It makes sure that
 # the vales in the table fall within the ENCODE Regions.
 #
 ################################
 
 set num=""
 set db=""
 set tablelist=""
 set count=""
 set column=""
 set theStart=""
 
 # usage statement
 if ( $#argv < 2 || $#argv > 3 ) then
   echo
   echo " Determines if all items in a table are within the ENCODE Regions."
   echo
   echo "  usage:  database tablelist [count]"
   echo "     (will accept single table)"
   echo "      where "count" gives list of count per chrom"
   echo
   exit
 else
   set db=$argv[1]
   set tablelist=$argv[2]
 endif
 
 if ( $#argv == 3 ) then
   set count=$argv[3]
   if ( "count" != $count ) then
     echo '\n ERROR: Third variable can only be "count".\n'
   endif
 endif
 
 # run this only on hgwdev
 if ( "$HOST" != "hgwdev" ) then
   echo "\n ERROR: you must run this script on dev!\n"
   exit 1
 endif
 
 # make sure this is an assembly that has encode tables
 if ( $db != hg16 && $db != hg17 && $db != hg18 ) then
   echo "\n ERROR: you must run this script on a db that has encode tables\n"
   exit 1
 endif
 
 # check if it is a file or a tablename
 file $tablelist | egrep -q "ASCII text" 
 if (! $status) then
   set tables=`cat $tablelist`
  else
   set tables=$tablelist
 endif
 
 # loop through all of the tables found in the previous statement.
 foreach tbl ($tables)  
   # make sure it's an encode table
   echo $tbl | egrep -q '^encode'
   if ( $status  ) then
    echo "\n ERROR: $tbl is not an ENCODE table\n"
    exit 1
   endif
 
   # if the table doesn't exist, print error and exit.
   set exists=`hgsql -Ne "SHOW TABLES LIKE '"$tbl"'" $db`
   if ( $exists == "" ) then
     echo "\n ERROR: The $tbl table does not exist in the $db database\n"
     exit 1
   endif
 
   # script doesn't work for encodeRegions table -- print error and exit.
   if ( $tbl == "encodeRegions" ) then
     echo "\n ERROR: This script doesn't work for the encodeRegions table!\n"
     exit 1
   endif
 
   # find out if the table has chromStart and/or txStart field 
   set column=`hgsql -Ne 'show columns from '$tbl' like "%Start"' $db`
 
   set theStart=`echo $column | awk '{print $1}'`
 
   switch ($theStart)
    case 'chromStart':
      set num=`hgsql -Ne 'SELECT count(*) FROM '$tbl', encodeRegions \
       WHERE '$tbl'.chrom = encodeRegions.chrom \
       AND '$tbl'.chromStart <= encodeRegions.chromStart \
       AND '$tbl'.chromEnd >= encodeRegions.chromEnd' $db`
      breaksw
    case 'txStart':
      set num=`hgsql -Ne 'SELECT count(*) FROM '$tbl', encodeRegions \
       WHERE '$tbl'.chrom = encodeRegions.chrom \ 
       AND '$tbl'.txStart <= encodeRegions.chromStart \
       AND '$tbl'.txEnd >= encodeRegions.chromEnd' $db`
      breaksw
    default:
      echo "\n ERROR: the $tbl table has no chromStart or txStart columns.\n"
      exit 1
      breaksw
   endsw
 
   if ($num != 0) then
     echo "\n ERROR: The $tbl table has $num items OUTSIDE of ENCODE Regions\n"
   else
     echo "\n$tbl table: OK\n"
   endif
 
   if ( $count == 'count') then
     echo "\nNumber of items per chromosome for $tbl table:\n"
     countPerChrom.csh $db $tbl
   endif
  
   set num=0
   set column=""
   set theStart=""
   set exists=""
 
 end #foreach
 exit