src/utils/qa/countPerChrom.csh 1.14

Index: src/utils/qa/countPerChrom.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/countPerChrom.csh,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/utils/qa/countPerChrom.csh	10 Jun 2009 15:33:33 -0000	1.13
+++ src/utils/qa/countPerChrom.csh	24 Jan 2010 06:56:41 -0000	1.14
@@ -1,140 +1,168 @@
 #!/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"
 
-if ( $#argv < 2 ||  $#argv > 4 ) then
+set debug=true 
+set debug=false
+
+if ( $#argv < 2 ||  $#argv > 5 ) then
   # no command line args
   echo
   echo "  check to see if there are annotations on all chroms."
   echo "  will check to see if chrom field is named tName or genoName."
   echo
-  echo "    usage:  database1 table [database2] [RR]"
+  echo "    usage:  database1 table [database2] [RR] [histogram]"
   echo
   echo "      checks database1 on dev"
   echo "      database2 will be checked on beta by default"
   echo "        if RR is specified, will use genome-mysql"
+  echo "        histogram will print only histogram and only for single db"
   echo
   exit
 else
   set db=$argv[1]
   set table=$argv[2]
 endif
 
 if ( $#argv == 3 ) then
+  if ( $argv[3] == "histogram" ) then
+    set histo="true"
+  else
   if ( $argv[3] == "RR" ) then
     set host2="mysql -h genome-mysql -u genome -A"
     set oldDb=$db
     set machineOut="(${argv[3]})"
   else
     set host2="hgsql -h $sqlbeta"
     set machineOut="(hgwbeta)"
+      if ( $argv[3] == "histogram" ) then
+      endif
     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 ( $#argv == 4 ) then
   set oldDb=$argv[3]
   set machineOut="(${argv[4]})"
   if ( $argv[4] == "hgwbeta" ) then
     set host2="hgsql -h $sqlbeta"
   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
+  endif
+endif
+
+if ( $#argv == 5 ) then
+  if ( $argv[5] == "histogram" ) then
+    set histo="true"
+  endif
 endif
 
-# echo "db = $db"
-# echo "oldDb = $oldDb"
-# echo "machineOut = $machineOut"
-# echo "table = $table"
-# echo "host2 = $host2"
+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 
 
-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`
 
+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 ( $machineOut != "" ) then
     set old=`$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$old"
+  echo "$c\t$new\t$old" >> Xout$$
   set table=$argv[2]
 end
 
+if ( $histo == "true" ) then
+  cat Xout$$ | egrep -v "random|hap|$db" | sed "s/chr//" | sort -n -k1,1  > XgraphFile$$
+  graph.csh XgraphFile$$ 
+  rm -f XgraphFile$$
+else
+  # output header
+  echo "chrom \t$db \t$oldDb$machineOut" 
+  cat Xout$$
+endif
+
+rm -f Xout$$