src/utils/qa/countPerChrom.csh 1.16

Index: src/utils/qa/countPerChrom.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/countPerChrom.csh,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 1000000 -r1.15 -r1.16
--- src/utils/qa/countPerChrom.csh	24 Jan 2010 19:45:16 -0000	1.15
+++ src/utils/qa/countPerChrom.csh	1 Feb 2010 05:12:48 -0000	1.16
@@ -1,186 +1,186 @@
 #!/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=""
 set histo="false"
 set histosize=35
 
 set debug=true 
 set debug=false
 
 if ( $#argv < 2 ||  $#argv > 5 ) then
   # no command line args
   echo
   echo "  check to see if there are annotations on all chroms."
   echo "  will check to see if chrom field is named tName or genoName."
   echo
   echo "    usage:  database1 table [database2] [RR] [histogram]"
   echo
   echo "      checks database1 on dev"
   echo "      database2 will be checked on beta by default"
   echo "        if RR is specified, will use genome-mysql"
   echo "      histogram option prints bar graph, not values"
   echo
   exit
 else
   set db=$argv[1]
   set table=$argv[2]
 endif
 
 if ( $#argv == 3 || $#argv == 4 ) then
   if ( $argv[3] == "histogram" ) then
     set histo="true"
   else
     if ( $argv[3] == "RR" || $argv[3] == "rr" ) then
       set host2="mysql -h genome-mysql -u genome -A"
       set oldDb=$db
       set machineOut="(${argv[3]})"
     else
       set host2="hgsql -h $sqlbeta"
       set machineOut="(hgwbeta)"
       if ( $argv[3] == "hgwbeta" ) then
         # allow use of "hgwbeta" to check same db in two places
         set oldDb=$db
       else
         # argv[3] must be a db
         set oldDb=$argv[3] 
       endif
     endif
   endif
 endif
 
 if ( $#argv > 3 ) then
   if ( $argv[4] == "histogram" ) then
     set histo="true"
   else
     set oldDb=$argv[3]
     set machineOut="(${argv[4]})"
     if ( $argv[4] == "hgwbeta" ) then
       set host2="hgsql -h $sqlbeta"
     else 
       if ( $argv[4] == "RR" || $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
   endif
 endif
 
 if ( $#argv == 5 ) then
   if ( $argv[5] == "histogram" ) then
     set histo="true"
   endif
 endif
 
 if ( $debug == true) then
   echo "db = $db"
   echo "oldDb = $oldDb"
   echo "machineOut = $machineOut"
   echo "table = $table"
   echo "host2 = $host2"
 endif
 
 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 
 
 # do randoms last (if no histogram)
 if ( $histo == "true" ) then
   set regular=`echo $chroms | sed -e "s/ /\n/g" | grep chr`
 else
   set regular=`echo $chroms | sed -e "s/ /\n/g" | grep -v random`
   set  random=`echo $chroms | sed -e "s/ /\n/g" | grep random`
 endif
 
 rm -f Xout$$
 rm -f XgraphFile$$
 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=`nice $host2 -Ne 'SELECT COUNT(*) FROM '$table' \
       WHERE '$chrom' = "'$c'"' $oldDb`
   endif 
   # output
   echo "$c\t$new\t$old" >> Xout$$
   set table=$argv[2]
 end
 
 if ( $histo == "true" ) then
-  cat Xout$$ | grep chr | egrep -v "random|hap|Un|$db" | sed "s/chr//" \
+  cat Xout$$ | grep chr | egrep -v "random|Un|$db" | sed "s/chr//" \
     | sort -n -k1,1  > XgraphFile$$
   if ( $machineOut != "" ) then
     cat XgraphFile$$ | awk '{print $1, $3}' > XgraphFile2$$ 
     graph.csh XgraphFile$$  $histosize > Xgraph1$$
     graph.csh XgraphFile2$$ $histosize > Xgraph2$$
     # output header
     echo
     echo "chr \t$db \t$oldDb$machineOut" | awk '{printf("%3s %'$histosize's %-'$histosize's\n", $1, $2, $3)}'
     # join on first col, retaining everything from first col
     join -a1 -j1 Xgraph1$$ Xgraph2$$ | awk '{printf("%3s %'$histosize's %-'$histosize's\n", $1, $2, $3)}'
   else
     graph.csh XgraphFile$$ | awk '{printf("%3s %-36s\n", $1, $2)}'
   endif
 else
   # output header
   echo "chrom \t$db \t$oldDb$machineOut" 
   cat Xout$$
 endif
 
 rm -f Xgraph1$$
 rm -f Xgraph2$$
 rm -f XgraphFile$$
 rm -f XgraphFile2$$
 rm -f Xout$$