src/utils/qa/countPerChrom.csh 1.5

Index: src/utils/qa/countPerChrom.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/countPerChrom.csh,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/utils/qa/countPerChrom.csh	24 Mar 2006 19:09:50 -0000	1.4
+++ src/utils/qa/countPerChrom.csh	3 Apr 2009 17:27:21 -0000	1.5
@@ -1,147 +1,147 @@
 #!/bin/tcsh
 
 ###############################################
 # 
 #  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 tableName=""
 set machine1="hgwdev"
 set machine2=""
 set host2=""
 set chrom="chrom"
 set chroms=""
 set old=""
 set new=""
 set onlyOne=0
 set machineOut=""
 set ok=0
 set split=""
 
 if ($#argv < 2 ||  $#argv > 4) then
   # no command line args
   echo
   echo "  check to see if there are genes on all chroms."
   echo "    will check to see if chrom field is named tName or genoName."
   echo
-  echo "    usage:  database, table, [oldDb], [other machine]"
+  echo "    usage:  database table [oldDb] [other machine]"
   echo "      where oldDb must be specified if other machine is used"
   echo "      oldDb will be checked on other machine"
   echo "      defaults to hgwdev"
   echo
   exit
 else
   set db=$argv[1]
   set table=$argv[2]
   set tableName=$table
 endif
 
 if ($#argv > 2) then
   set oldDb=$argv[3]
 else
   set onlyOne=1
 endif
 
 if ($#argv == 4) then
   set oldDb=$argv[3]
   set machine1=$argv[4]
   set machine2=$argv[4]
   set machineOut="(${argv[4]})"
   set host2="-h $argv[4]"
 endif
 
 # echo "db = $db"
 # echo "oldDb = $oldDb"
 # echo "machine2 = $machine2"
 # echo "table = $table"
 
 set chroms=`hgsql -N -e "SELECT chrom FROM chromInfo" $db`
 set split=`getSplit.csh $db $table $machine1`
 if ($status) then
   echo "\n  maybe the database is not present on $machine1?\n"
   exit
 endif
 
 if ($split != "unsplit") then
   set tableName=${split}_$table
   echo "\nsplit tables. e.g., $tableName"
 endif
 
 # check if maybe chrom is called tName
 hgsql -e "DESC $tableName" $db | egrep -w tName > /dev/null 
 if (! $status ) then
   set chrom="tName"
   echo 'chrom is "tName"'
   set ok=1
 endif 
 
 # check if maybe chrom is called genoName (prob only rmsk)
 hgsql -e "DESC $tableName" $db | egrep -w genoName > /dev/null 
 if (! $status ) then
   set chrom="genoName"
   echo 'chrom is "genoName"'
   set ok=1
 endif 
 
 # final check to see chrom-like field present
 hgsql -e "DESC $tableName" $db | egrep -w chrom > /dev/null 
 if (! $status ) then
   set ok=1
 endif 
 
 if ($ok == 0) then
   echo
   echo " no appropriate field for this table."
   echo "   chrom, genoName or tName required."
   echo
   exit
 endif 
 
 echo
 
 # output header
 echo "chrom \t$db \t$oldDb$machineOut"
 
 foreach x (`echo $chroms | sed -e "s/ /\n/g" | grep -v random`)
   if ($split != "unsplit") then
     set table="${x}_$table"
   endif
   set new=`nice hgsql -N -e 'SELECT COUNT(*) FROM '$table' \
      WHERE '$chrom' = "'$x'"' $db`
   if ($onlyOne == 0) then
     set old=`nice hgsql -N $host2 -e 'SELECT COUNT(*) FROM '$table' \
       WHERE '$chrom' = "'$x'"' $oldDb`
   endif 
   # output
   echo "$x\t$new\t$old"
   set table=$argv[2]
 end
 
 # do randoms separately
 foreach x (`echo $chroms | sed -e "s/ /\n/g" | grep random`)
   if ($split != "unsplit") then
     set table="${x}_$table"
   endif
   set new=`nice hgsql -N -e 'SELECT COUNT(*) FROM '$table' \
      WHERE '$chrom' = "'$x'"' $db`
   if ($onlyOne == 0) then
     set old=`nice hgsql -N $host2 -e 'SELECT COUNT(*) FROM '$table' \
       WHERE '$chrom' = "'$x'"' $oldDb`
   endif
   echo "$x\t$new\t$old"
   set table=$argv[2]
 end