Index: src/utils/qa/countPerChrom.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/countPerChrom.csh,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 1000000 -r1.9 -r1.10
--- src/utils/qa/countPerChrom.csh	22 May 2009 21:58:32 -0000	1.9
+++ src/utils/qa/countPerChrom.csh	28 May 2009 17:09:38 -0000	1.10
@@ -1,128 +1,134 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 ###############################################
 # 
 #  12-13-05
 #  Robert Kuhn
 #
 #  check to see if there are genes on all chroms.
 # 
 ###############################################
 
 
 if ( "$HOST" != "hgwdev" ) then
  echo "\n  error: you must run this script on dev!\n"
  exit 1
 endif
 
 set db=""
 set oldDb=""
 set table=""
 set host2=""
 set chrom=""
 set chroms=""
 set old=""
 set new=""
 set machineOut=""
 set split=""
 set regular=""
 set random=""
 
 if ( $#argv < 2 ||  $#argv > 4 ) then
   # no command line args
   echo
   echo "  check to see if there are annotations on all chroms."
   echo "    will check to see if chrom field is named tName or genoName."
   echo
   echo "    usage:  database1 table [database2] [RR]"
   echo
   echo "      checks database1 on dev"
   echo "      database2 will be checked on beta by default"
   echo "        RR will use genome-mysql if specified"
   echo
   exit
 else
   set db=$argv[1]
   set table=$argv[2]
 endif
 
 if ( $#argv == 3 ) then
   if ( $argv[3] == "RR" ) then
     set host2="mysql -h genome-mysql -u genome -A"
     set oldDb=$db
     set machineOut="(${argv[3]})"
   else
     # argv[3] must be a db
     set oldDb=$argv[3] 
     set host2="hgsql -h $sqlbeta"
     set machineOut="(hgwbeta)"
   endif
 endif
 
 if ( $#argv == 4 ) then
   set oldDb=$argv[3]
   set machineOut="(${argv[4]})"
   if ( $argv[4] == "hgwbeta" ) then
     set host2="hgsql -h $sqlbeta"
-  endif
+  else 
   if ( $argv[4] == "RR" ) then
     set host2="mysql -h genome-mysql -u genome -A"
+    else
+      echo
+      echo "4th parameter must be RR or hgwbeta"
+      echo
+      $0
+      exit 1
   endif
 endif
 
 # echo "db = $db"
 # echo "oldDb = $oldDb"
 # echo "machineOut = $machineOut"
 # echo "table = $table"
 # echo "host2 = $host2"
 
 set chroms=`hgsql -N -e "SELECT chrom FROM chromInfo" $db`
 set split=`getSplit.csh $db $table`
 if ( $status ) then
   echo "\n  the database or table may not exist\n"
   exit
 endif
 
 if ( $split == "unsplit" ) then
   set split=""
 else
   set split=${split}_
   echo "\n  split tables. e.g., $split$table"
 endif
 
 set chrom=`getChromFieldName.csh $db $split$table`
 if ( $status ) then
   echo "  error getting chromFieldName."
   echo "   chrom, genoName or tName required."
   echo
   exit 1
 endif 
 
 echo
 
 # output header
 echo "chrom \t$db \t$oldDb$machineOut"
 
 # do randoms last
 set regular=`echo $chroms | sed -e "s/ /\n/g" | grep -v random`
 set  random=`echo $chroms | sed -e "s/ /\n/g" | grep random`
 
 foreach c ( $regular $random )
   if ( $split != "" ) then
     set table="${c}_$table"
   endif
   set new=`nice hgsql -N -e 'SELECT COUNT(*) FROM '$table' \
      WHERE '$chrom' = "'$c'"' $db`
   if ( $machineOut != "" ) then
     set old=`$host2 -Ne 'SELECT COUNT(*) FROM '$table' \
       WHERE '$chrom' = "'$c'"' $oldDb`
     set old=`nice $host2 -Ne 'SELECT COUNT(*) FROM '$table' \
       WHERE '$chrom' = "'$c'"' $oldDb`
   endif 
 
   # output
   echo "$c\t$new\t$old"
   set table=$argv[2]
 end
 

