src/utils/qa/getYield.csh 1.3

Index: src/utils/qa/getYield.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/getYield.csh,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/utils/qa/getYield.csh	11 Jan 2006 23:08:13 -0000	1.2
+++ src/utils/qa/getYield.csh	11 Apr 2009 00:37:04 -0000	1.3
@@ -1,105 +1,106 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 ####################
 #  05-03-04 Bob Kuhn
 #
 #  Script to process use featureBits to get yield and enrichment
 #
 ####################
 
 if ( "$HOST" != "hgwdev" ) then
  echo "\n error: you must run this script on dev!\n"
  exit 1
 endif
 
 
 set track=""
 set refTrack=""
 set db=""
 set current_dir = $cwd
 set uniqFlag=0
 
 if ($#argv < 2 || $#argv > 3) then
   # not enough command line args
   echo
   echo "  uses featureBits to get yield and enrichment."
   echo
   echo "    usage:  database, trackname, [reference track] defaults to refGene"
   echo
   exit
 else
   set db=$argv[1]
   set track=$argv[2]
   set refTrack="refGene"
 endif
 
 if ($#argv == 3) then
   set refTrack=$argv[3]
 endif
 
 echo
 echo "database: $db"
 echo "track: $track"
 echo "reference track: $refTrack"
 
 hgsql -N -e "SHOW TABLES" $db | grep -w $track > /dev/null
 if ($status) then
   echo "\n  error. table $track not found in $db\n"
   exit
 endif
 
 hgsql -N -e "SHOW TABLES" $db | grep -w $refTrack > /dev/null
 if ($status) then
   echo "\n  error. table $refTrack not found in $db\n" 
   exit
 endif
 
 
 # -------------------------------------------------
 # check featureBits:
 
 echo
 echo "$track"
 featureBits $db $track >& thisTrack
 cat thisTrack
 echo
 echo "${refTrack}:cds"
 featureBits $db ${refTrack}:cds >& $refTrack 
 cat $refTrack
 echo
 echo "intersection of $track with ${refTrack}:cds"
 featureBits $db ${refTrack}:cds $track >& union
 cat union
 echo
 
 set thisTrack=`cat thisTrack | gawk '{print $1}'`
 set genome=`cat thisTrack | gawk '{print $4}'`
 set ref=`cat $refTrack | gawk '{print $1}'`
 cat $refTrack
 set union=`cat union | gawk '{print $1}'`
 
 set yield=`echo $union $ref \
      | gawk '{printf "%.1f\n", $1/$2*100}'`
 set enrichment=`echo $union $thisTrack $ref $genome \
      | gawk '{printf "%.1f\n", ($1/$2)/($3/$4)}'`
 
 # yield is what portion of the reference track was captured in the
 #    other track
 # enrichment is how many times better this track overlaps the reference
 #    track than that track's proportion of the genome (I think)
 
 echo "thisTrack = $thisTrack"
 echo "refTrack  = $ref"
 echo "union     = $union"
 echo "genome  = $genome"
 echo
 echo "yield       = ${yield}% (union / $refTrack)"
 echo "enrichment  = ${enrichment}x ((union / $track) / ($refTrack / genome))"
 echo
 
 rm union
 rm thisTrack
 rm $refTrack