src/utils/qa/doGenbankTests 1.2

Index: src/utils/qa/doGenbankTests
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/doGenbankTests,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/utils/qa/doGenbankTests	10 Apr 2009 20:37:55 -0000	1.1
+++ src/utils/qa/doGenbankTests	10 Apr 2009 21:53:45 -0000	1.2
@@ -1,159 +1,157 @@
 #!/bin/bash -e
 ###############################################################################
 #  doGenbankTests
 #
 #  June 2008 -- Brooke Rhead
 #
 #  Wrapper script for automated checking of GenBank tables.
 #  Note: this script assumes the kent source tree is checked out in ~/kent/src
 # 
 ###############################################################################
 
 tableExists()
 {
   local db=$1
   local table=$2
   local res=`hgsql -Ne "show tables like '$table'" $db`
   if [ -z "$res" ]
   then
     return 1 
   else
     return 0
   fi
 }
 
 allOk=yes
 
 # check host, set path to genbank table list
 if [ "$HOST" != hgwdev -a "$HOST" != hgwbeta ]
 then
   echo "This script must be run from hgwdev or hgwbeta." >&2
   exit 1
 elif [ "$HOST" = hgwdev ]
 then
   genbankPath="/cluster/data/genbank/etc/genbank.tbls"
   sanityPath="/cluster/data/genbank"
 else #host is hgwbeta
   genbankPath="/genbank/etc/genbank.tbls"
   sanityPath="/genbank"
 fi
 
 # get arguments / give usage statement
 if [ $# -lt 1 -o $# -gt 2 ]
 then
   echo "usage:  $(basename $0) db [outFile]
 where outFile is the name of a file in which to record results" >&2
   exit 1
 else
   db="$1"
   if [ $# -eq 2 ]
   then
     exec > "$2" 2>&1  # neat bash trick to redirect stdout (also redirecting error)
   fi
 fi
 
 # print some useful info
 echo "$(basename $0) output on $db"
 date
 echo
 
 # get a list of all genbank tracks present in this assembly
 echo "The following GenBank tracks are present in this assembly:"
 
 # now look for the actual tracks
 tableExists $db refGene && trackList="${trackList} refGene" && echo -e "\tRefSeq Genes"
 tableExists $db xenoRefGene && trackList="${trackList} xenoRefGene" && echo -e "\tOther RefSeq"
 tableExists $db all_mrna && trackList="${trackList} all_mrna" && echo -e "\t\$Org mRNAs"
 tableExists $db xenoMrna && trackList="${trackList} xenoMrna" && echo -e "\tOther mRNAs"
 tableExists $db all_est && trackList="${trackList} all_est" && echo -e "\t\$Org ESTs"
 tableExists $db %intronEst && trackList="${trackList} %intronEst" && echo -e "\tSpliced ESTs"
 tableExists $db xenoEst && trackList="${trackList} xenoEst" && echo -e "\tOther ESTs"
 tableExists $db mgcGenes  && trackList="${trackList} mgcGenes"&& echo -e "\tMGC Genes"
 tableExists $db orfeomeGenes  && trackList="${trackList} orfeomeGenes"&& echo -e "\tORFeome Clones"
 echo
 
 echo -e "--> Running genePredCheck and pslCheck:\n"
 
 # run genePredChecks
 for table in refGene xenoRefGene mgcGenes orfeomeGenes
 do
   tableExists $db $table && {
     echo genePredCheck $table
     nice genePredCheck -db=$db $table || allOk=no
   }
 done
 echo
 
 # run pslChecks
 for table in all_mrna xenoMrna all_est refSeqAli xenoRefSeqAli
 do
   tableExists $db $table && {
     echo pslCheck $table
     nice pslCheck -db=$db $table || allOk=no
   }
 done
 echo
 
 # run joinerCheck
 joinerLoc=~/kent/src/hg/makeDb/schema/all.joiner
 
 echo -e "--> Checking appropriate keys in $(basename $joinerLoc):\n"
 
 doJoinerCheck() {
   local table=$1 ident=$2
   tableExists $db $table && {
     echo joinerCheck -keys -database=$db -identifier=$ident $(basename $joinerLoc)
     nice joinerCheck -keys -database=$db -identifier=$ident $joinerLoc || allOk=no
     echo
   }
 }
 
 doJoinerCheck gbCdnaInfo gbCdnas
 doJoinerCheck refGene refSeqId
 doJoinerCheck xenoRefGene xenoRefSeqId
 doJoinerCheck all_mrna nativeMrnaAccession
 doJoinerCheck xenoMrna xenoMrnaAccession
 doJoinerCheck all_est nativeEstAccession # takes care of intronEst, too
 doJoinerCheck xenoEst xenoEstAccession
 doJoinerCheck mgcGenes mgcAccession
 doJoinerCheck orfeomeGenes orfeomeAccession
 echo
 
 # run gbSanity
 timestamp=$(date +%m.%d.%Y-%R%p)
 echo -e "--> Running gbSanity, and putting output in:"
 echo -e "${HOST}:${sanityPath}/misc/${db}.sanity.$timestamp"
-oldPath=$(pwd)
-cd ${sanityPath}
-bin/x86_64/gbSanity $db >& misc/${db}.sanity.$timestamp || allOk=no
-cd $oldPath
+(cd ${sanityPath} && bin/x86_64/gbSanity $db >& misc/${db}.sanity.$timestamp) || allOk=no
 echo -e "Here is the last line of ${db}.sanity.$timestamp:\n"
 tail -1
 echo -e "If there are any errors here, consult Mark Diekhans.\n"
 
 # run featureBits
 echo -e "--> Running featureBits.  Remember to paste this into the pushqueue:\n"
 for table in refGene xenoRefGene mgcGenes all_mrna intronEst all_est xenoMrna mgcFullMrna orfeomeGenes
 do
   tableExists $db $table && {
     echo featureBits -countGaps $db $table
     nice featureBits -countGaps $db $table || allOk=no
     echo featureBits -countGaps $db $table gap
     nice featureBits -countGaps $db $table gap || allOk=no
     echo
   }
 done
 echo
 
 # run countPerChrom??
 
 # give overall report of errors
 if [ $allOk = yes ]
 then
   echo No errors were encountered during $(basename $0).  Yay!
+  date
 else
   echo At least one ERROR occurred during $(basename $0).
+  date
   exit 2
 fi
 exit 0
-# end.