src/utils/qa/findDbPartners.csh 1.8

Index: src/utils/qa/findDbPartners.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/findDbPartners.csh,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 1000000 -r1.7 -r1.8
--- src/utils/qa/findDbPartners.csh	24 Mar 2009 19:10:44 -0000	1.7
+++ src/utils/qa/findDbPartners.csh	11 Apr 2009 00:37:03 -0000	1.8
@@ -1,76 +1,77 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 #######################
 #
 #  08-22-08
 #  gets the names of all databases that have associations with a database
 #
 #######################
 
 set db=""
 set fullDbList=""
 set net=""
 
 if ( "$HOST" != "hgwdev" ) then
  echo "\n error: you must run this script on dev!\n"
  exit 1
 endif
 
 if ( $#argv != 1 ) then
   echo
   echo "  gets the names of all databases that have associations with a database"
   echo
   echo "    usage:  database"
   echo
   echo "    runs on hgwbeta"
   echo
   exit
 else
   set db=$argv[1]
 endif
 
 # uppercase the db, make net name and find any assemblies with nets to db
 set Db=`echo $db | perl -wpe '$_ = ucfirst($_)'`
 set net="net$Db"
 getAssemblies.csh $net  | grep -v hgwbeta | tee $db.fullList
 
 # get multiz tracks in other assemblies
 echo "conservation:"
 getConservation.csh $db | tee -a $db.fullList
 
 # get {Human,Fly,Worm} Proteins tracks in other assemblies
 getAssemblies.csh blast%${Db}% | egrep -v "found|split" | tee -a $db.fullList 
 
 # find if {Human,Fly,Worm} Proteins track exists
 echo "find if {Human,Fly,Worm} Proteins track exists.  ref to:"
-hgsql -h hgwbeta -e "SHOW TABLES LIKE 'blast%'" $db | egrep "FB|KG|SG" \
+hgsql -h $sqlbeta -e "SHOW TABLES LIKE 'blast%'" $db | egrep "FB|KG|SG" \
   | egrep -v "Ref|Pep" \
   | sed "s/blast//" | perl -pwe '$_ = lcfirst($_)' | perl -wpe "s/FB|KG|SG//" \
   | tee -a $db.fullList
 echo
 
 # get liftOvers:
 getLiftOver.csh $db hgwbeta | tee -a $db.liftOverList
 echo
 
 echo "------------"
 # get hgGene connections (blastTab)
 echo "knownGenes using $db (blastTab):"
 find ~/kent/src/hg/hgGene -name otherOrgs.ra | xargs grep $db \
   | awk -F":" '{print $1}' > $db.kgList
 sed "s/\// /g" $db.kgList  | awk '{print $(NF-1)}' | sort 
 echo
 
 echo "------------"
 echo "liftOver set:"
 cat $db.liftOverList | egrep -v "chains" | awk '{print $1}' | grep . | sort -u
 
 echo
 echo "------------"
 echo "unique set of assemblies with connecting tracks:"
 cat $db.fullList | egrep -v "blast|found" | awk '{print $1}' | grep . | sort -u
 echo
 
 rm -f $db.*List
 exit 0