src/utils/qa/qaThis.csh 1.1

Index: src/utils/qa/qaThis.csh
===================================================================
RCS file: src/utils/qa/qaThis.csh
diff -N src/utils/qa/qaThis.csh
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/utils/qa/qaThis.csh	9 Apr 2010 00:16:28 -0000	1.1
@@ -0,0 +1,169 @@
+#!/bin/tcsh
+source `which qaConfig.csh`
+
+# This script runs qa scripts on a table
+
+# enter the name of the database and the name of the table
+
+set db=''
+set tableList=''
+set table =''
+set first=""
+set second=""
+#set third=""
+set fourth=""
+set countPerChr=""
+
+if ($#argv < 2 || $#argv > 3) then
+  echo
+  echo " Runs basic QA scripts on your table(s)"
+  echo
+  echo "    usage:  database Tablename [c]"
+  echo
+  echo "    c should run count per chrom" 
+  echo "    Creates files if given multiple tables!"
+  echo "    Runs countPerChrom last so if it gets scaffold-y"
+  echo "    Or you just don't care, you can just stop looking"
+  echo
+  echo "    If you happen to have ideas on how to make it simply not run"
+  echo "    When it's scaffolds versus actual chroms, let me know"                                        
+  echo
+  echo "    It should also work if you provide a list"
+  echo "    I make no promises though"
+
+  exit
+else
+  set db=$argv[1]
+  set tableList=$argv[2]
+  
+  if ( $#argv == 3 ) then
+    set countPerChr=$argv[3]
+  endif
+endif
+
+if ( "$HOST" != "hgwdev" ) then
+ echo "\n  error: you must run this script on dev!\n"
+ exit 1
+endif
+
+file $tableList | egrep "ASCII text" > /dev/null
+if (! $status) then
+ set tables=`cat $tableList`
+ if ( $countPerChr != "c" ) then
+   foreach table ( $tables )
+     $0 $db $table >& $db.$table.qa
+   end
+ else  
+   foreach table ( $tables )
+     $0 $db $table c >& $db.$table.qa
+   end
+ endif  
+else
+  set tables=$tableList
+
+#------------------------------------------------
+#check getSplit.csh 
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "Is this table split (using getSplit.csh)"
+
+getSplit.csh $db $tables hgwdev 
+
+# ------------------------------------------------
+# check updateTimes for each table:
+
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo
+set first=`hgsql -N -e 'SHOW TABLE STATUS LIKE "'$tables'"' $db \
+   | awk '{print $14, $15}'`
+set second=`hgsql -h $sqlbeta -N -e 'SHOW TABLE STATUS LIKE "'$tables'"' $db \
+   | awk '{print $14, $15}'`
+set fourth=`getRRtableStatus.csh $db $tables Update_time`
+if ( $status ) then
+    set fourth=""
+endif    
+echo "Check updateTimes for each table:"
+echo "Dev:  $first "
+echo "Beta: $second"
+echo "RR:   $fourth" 
+
+# ------------------------------------------------
+# check FeatureBits for table:
+
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "Check FeatureBits(second is vs. gap) : "
+echo "featureBits -countGaps $db $tables"
+featureBits -countGaps $db $tables
+
+if ($status) then
+  echo "failed."
+  echo
+endif
+
+echo "featureBits -countGaps $db $tables gap"
+featureBits -countGaps $db $tables gap -bed=$db.$tables.gapFile
+echo
+if ( -z $db.$tables.gapFile ) then
+echo
+rm -f $db.$tables.gapFile
+else
+echo "There are gaps overlapping $tables (gaps may be bridged or not):"
+echo "Gap file is here: $db.gapFile" 
+endif
+		    
+# ------------------------------------------------
+# check Table sort for table:
+
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "Check table sort:"
+positionalTblCheck $db $tables
+
+# ------------------------------------------------
+# check if any values are off Chrom ends
+
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "Check whether entries are off chroms:"
+checkOffend.csh $db $tables
+
+#----------------------------------------------
+#Check indeces
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "check indeces:"
+hgsql -e "show index from ${tables}" $db
+
+#-----------------------------------------------
+#joiner check
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "Joiner check:"
+runJoiner.csh $db $tables noTimes
+
+# ------------------------------------------------
+# check level for html and trackDb entry:
+
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "check level for html and trackDb entry:"
+findLevel $db $tables
+
+# ------------------------------------------------
+#Verify make doc:
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "Verify the makedoc at:"
+echo "~/kent/src/hg/makeDb/doc/$db.txt"
+
+#----------------------------------------------
+#Show the first 2 rows
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "Here are the first two rows of the table:"
+hgsql -e "select * from ${tables} limit 2" $db
+
+#------------------------------------------------
+#Count per Chrom 
+  if ( $countPerChr == "c" ) then
+    echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+    echo "Check countPerChrom.csh"  
+    countPerChrom.csh $db $tables
+  endif
+endif
+
+exit 0
+
+