src/utils/qa/findMtNets.csh 1.5

Index: src/utils/qa/findMtNets.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/findMtNets.csh,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/utils/qa/findMtNets.csh	23 May 2008 18:44:34 -0000	1.4
+++ src/utils/qa/findMtNets.csh	11 Apr 2009 00:37:03 -0000	1.5
@@ -1,96 +1,97 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 
 ###############################################
 # 
 #  05-13-08
 #  Robert Kuhn
 #
 #  Finds all scaffolds or contigs that have no chain/net to any of
 #    of the comparative tracks in otherOrgs
 # 
 ###############################################
 
 
 set db=""
 set dbList=""
 set count=""
 set flag=""
 
 if ($#argv != 2) then
   # no command line args
   echo
   echo "  finds all scaffolds or contigs that have no chain/net to any other orgs."
   echo
   echo "    usage:  database fileOfOtherDbNames"
   echo
   echo "    note:  expects db.net.OtherOrg output from chainNetTrio down one directory"
   echo "           though not necessarily all in the same directory"
   echo
   exit
 else
   set db=$argv[1]
   set dbList=$argv[2]
   if ( ! -e $dbList ) then
     echo "  ${dbList}: no such file"
     exit 1
   endif
 endif
 
 set count=`grep -c . $dbList`
 
 foreach otherDb (`cat $dbList`)
   set capDb=`echo $otherDb | perl -wpe '$_ = ucfirst($_)'`
   if ( -e $dbList ) then
     test */$db.net.$capDb  >& /dev/null
     if ( $status ) then
       echo
       echo " no file:  */$db.net.$capDb"
       echo " proceeding without it "
       set count=`expr $count - 1`
       set flag="$flag\n Note:  not all net files were present, including for $otherDb"
     else
       ls */$db.net.$capDb  | xargs grep 'is empty' | awk '{print $1}' > $otherDb.mtNet
     endif
   endif
 end
 
 echo
 echo "number of empty nets:"
 wc -l *mtNet | grep -v total
 echo "number of chroms:"
 hgsql -N -e "SELECT COUNT(*) FROM chromInfo" $db | tail -1
 echo
 
 echo "find nets that are empty in all nets:"
 rm -f mtNetAll
 foreach otherDb (`cat $dbList`)
   cat $otherDb.mtNet >> mtNetAll
 end
 sort mtNetAll | uniq -c | sort -nr | head -10
 
 echo
 echo "number of chroms empty in all $count otherOrg nets:"
 sort mtNetAll | uniq -c | sort -nr | grep -w $count | awk '{print $2}' > $db.mtNetList
 wc -l $db.mtNetList | awk '{print $1}'
 echo
 
 echo "list of sizes of mtNets:"
 echo '#chrom    #size' > $db.mtNetSizes
 hgsql -N -e "SELECT chrom, size FROM chromInfo" $db | grep -f $db.mtNetList  >> $db.mtNetSizes
 wc -l $db.mtNetSizes | awk '{print $1-1, $2}'
 echo
 head -6 $db.mtNetSizes
 echo "..."
 tail -5 $db.mtNetSizes
 echo
 
 echo "total size:"
 cat $db.mtNetSizes | awk '{total+=$2} END {print total/1000000}'
 echo "(megabases)"
 
 echo $flag
 
 echo
 rm -f mtNetAll
 rm -f $db.mtNetList