src/utils/qa/getConservation.csh 1.5

Index: src/utils/qa/getConservation.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/getConservation.csh,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/utils/qa/getConservation.csh	18 Oct 2007 20:36:25 -0000	1.4
+++ src/utils/qa/getConservation.csh	21 Mar 2009 00:29:25 -0000	1.5
@@ -1,111 +1,111 @@
 #!/bin/tcsh
 
 #######################
 #
 #  10-30-06
 #  get the assemblies that use a particular db in the Conservation track.
 #
 #  Robert Kuhn and Brooke Rhead
 #
 #######################
 
 set tablename=""
 set machine="hgwbeta"
-set host="-h hgwbeta"
+set host="-h hgofbeta"
 set db=""
 set dbs=""
 set all=0
 
 if ( "$HOST" != "hgwdev" ) then
  echo "\n error: you must run this script on dev!\n"
  exit 1
 endif
 
 if ($#argv < 1 || $#argv > 2 ) then
   echo
   echo "  get the assemblies that use a particular db in the Conservation track."
   echo
   echo "    usage:  db|all [hgwdev|hgwbeta] "
   echo
   echo '             where "all" prints species list for all tracks in all dbs.'
   echo "             does not work on RR machines."
   echo "             defaults to beta"
   echo
   exit
 endif
 
 set debug=0
 
 # assign command line arguments
 
 if ($argv[1] == "all" ) then
   set all=1
 else
   set db=$argv[1]
 endif
 
 if ($#argv == 2 ) then
   set machine="$argv[2]"
   set host="-h $argv[2]"
   if ($argv[2] == "hgwdev") then
     set host=""
   endif
 endif
 
 if ($machine != "hgwdev" && $machine != "hgwbeta" ) then
   echo "\n  Sorry, only works for hgwdev and hgwbeta \n"
   exit 1
 endif
 
 # check machine validity
 checkMachineName.csh $machine
 if ( $status ) then
   echo "${0}:"
   $0
   exit 1
 endif
 
 if ($debug == 1) then
   echo "tablename = $tablename"
   echo "machine   = $machine"
   echo "host      = $host"
   echo "db        = $db"
   echo "rr        = $rr"
   echo "dumpDate  = $dumpDate"
   echo
 endif
 
 # -------------------------------------------------
 # get all assemblies containing multiz% or mz%
 
 set dbs=`getAssemblies.csh multiz% $machine | grep -v "multiz" | egrep "."`
 set dbs2=`getAssemblies.csh mz% $machine | grep -v "mz" | egrep "."`
 set dbs=`echo $dbs $dbs2`
 
 echo
 foreach assembly ( $dbs )
   set multilist=`hgsql $host -N -e "SELECT tableName FROM trackDb \
      WHERE tableName LIKE 'multiz%' OR tableName LIKE 'mz%'" $assembly` 
   if ( $all == 1) then
     foreach table ( $multilist )
       echo $assembly $table
       echo "-------"
       hgsql $host -N -e 'SELECT settings FROM trackDb \
          WHERE tableName = "'$table'"' $assembly | sed -e "s/\\n/\n/g" \
          | egrep "^sGroup|speciesOrder" | sed -e "s/ /\n/g" \
          | egrep -v "^sGroup|speciesOrder"
       echo "=========================="
     end
   else
     foreach table ( $multilist )
       hgsql $host -N -e 'SELECT settings FROM trackDb \
          WHERE tableName = "'$table'"' $assembly | sed -e "s/\\n/\n/g" \
          | egrep "^sGroup|speciesOrder" | sed -e "s/ /\n/g" \
          | egrep -v "^sGroup|speciesOrder" | grep $db > /dev/null
       if (! $status ) then
         echo "$assembly $table" | awk '{printf("%-7s  %-25s\n", $1, $2)}'
       endif
     end
   endif
 end
 echo