src/utils/qa/qaEncodeTracks.csh 1.1

Index: src/utils/qa/qaEncodeTracks.csh
===================================================================
RCS file: src/utils/qa/qaEncodeTracks.csh
diff -N src/utils/qa/qaEncodeTracks.csh
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/utils/qa/qaEncodeTracks.csh	28 Jul 2009 16:04:10 -0000	1.1
@@ -0,0 +1,137 @@
+#!/bin/tcsh
+
+###############################################
+# 
+#  03-05-2009
+#  Ann Zweig
+#
+#  Runs through the usual checks for ENCODE
+#  tables.
+# 
+###############################################
+
+set db=''
+set tableList=''
+
+if ($#argv != 2 ) then
+  echo
+  echo "  runs test suite for ENCODE tracks"
+  echo "  (it's best to direct output and errors to a file: '>&')"
+  echo
+  echo "    usage: db tableList"
+  echo
+  exit 1
+else
+  set db=$argv[1]
+  set tableList=$argv[2]
+endif
+
+# run only from hgwdev
+if ( "$HOST" != "hgwdev" ) then
+  echo "\nERROR: you must run this script on hgwdev!\n"
+  exit 1
+endif
+
+# check to see if it is a single tableName or a tableList
+file $tableList | egrep "ASCII text" > /dev/null
+if (! $status) then
+ set tables=`cat $tableList`
+else
+ set tables=$tableList
+endif
+
+
+# featureBits for all tables
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** featureBits for all tables ***"
+foreach table ( $tables )
+ echo ""
+ echo "featureBits -countGaps $db $table"
+ nice featureBits -countGaps $db $table
+ echo "featureBits -countGaps $db $table gap"
+ nice featureBits -countGaps $db $table gap
+end
+
+# check for table descriptions for all tables
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** check for tableDescription entry for all tables ***"
+echo "Is there an entry in the tableDescriptions table for each"
+echo "table? (1 == yes, 0 == no)"
+foreach table ( $tables )
+ echo ""
+ echo "Table: $table"
+ hgsql -Ne "select count(*) from tableDescriptions where tableName = '$table'" $db
+end
+
+# no underscores in table names
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** make sure there are no underscores in table names ***"
+echo "If there's output here, you have one or more tables with "_":"
+echo $tables | grep "_"
+echo ""
+
+# check that positional tables are sorted for all tables
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** check that positional tables are sorted ***"
+echo "(No output means table is sorted)"
+foreach table ( $tables )
+ echo ""
+ echo "positionalTblCheck $db $table"
+ positionalTblCheck $db $table
+end
+
+# check table index for each table
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** Check table INDEX ***"
+foreach table ( $tables )
+ echo ""
+ echo ""
+ hgsql -e "SHOW INDEX FROM $table" $db
+end
+
+# checkTableCoords for each table (instead of checkOffend.csh)
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** checkTableCoords for each table ***"
+foreach table ( $tables )
+ checkTableCoords $db $table
+end
+echo "\n(Nothing will be printed if all are okay.)"
+
+# check the length of the shortLabel for each track
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** MAX length of shortLabel should be 16 ***"
+foreach table ( $tables )
+ echo "Table: $table"
+ cat ~/trackDb/human/hg18/trackDb.wgEncode.ra | grep -A10 "track $table" | grep shortLabel \
+  | sed -e 's/shortLabel //' | sed -e 's/^ *//' | sed -e 's/.$//' | wc -m
+end
+
+# check the length of the longLabel for each track
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** MAX length of longLabel should be 80 ***"
+foreach table ( $tables )
+ echo "Table: $table"
+ cat ~/trackDb/human/hg18/trackDb.wgEncode.ra | grep -A10 "track $table" | grep longLabel \
+  | sed -e 's/longLabel //' | sed -e 's/^ *//' | sed -e 's/.$//' | wc -m
+end
+
+# countPerChrom for all tables
+echo "\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "*** countPerChrom for all tables ***"
+foreach table ( $tables )
+ echo ""
+ echo "countPerChrom.csh $db $table"
+ countPerChrom.csh $db $table
+end
+
+echo "\nthe end.\n"
+exit 0