src/utils/qa/checkWigFiles.csh 1.1

Index: src/utils/qa/checkWigFiles.csh
===================================================================
RCS file: src/utils/qa/checkWigFiles.csh
diff -N src/utils/qa/checkWigFiles.csh
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/utils/qa/checkWigFiles.csh	23 Apr 2009 23:39:28 -0000	1.1
@@ -0,0 +1,70 @@
+#!/bin/tcsh
+source `which qaConfig.csh`
+
+################################
+#
+# 04-23-2009
+# Ann Zweig
+#
+# This script is used to check wiggle files. It accepts a table name
+# that has a wiggle file associated with it. It makes sure that the wiggle 
+# file corresponds correctly with its table.
+#
+################################
+
+set db=""
+set table=""
+set file=""
+set remove="F"
+
+# usage statement
+if ( $#argv < 3 || $#argv > 4 ) then
+ echo
+ echo " Ensures that a table correlates with its wig file."
+ echo " Only prints results if there is a problem."
+ echo
+ echo "  usage:  database tableName fileName [rm]"
+ echo "   fileName includes path of wig download file "
+ echo "    (.txt and/or .gz files are OK)"
+ echo
+ echo "    e.g. /goldenPath/<db>/wig/fileName.wig"
+ echo
+ echo "    add rm if you would like the output files to be removed."
+ echo
+ exit
+else
+ set db=$argv[1]
+ set table=$argv[2]
+ set file=$argv[3]
+ if ( 4 == $#argv ) then
+  set remove="T"
+ endif
+endif
+
+if ( "$HOST" != "hgwdev" ) then
+ echo "\nERROR: this script must be run from hgwdev."
+ exit 1
+endif
+
+if ( ! -e $file ) then
+ echo " \nERROR: sorry I can't find the original wig file here: ~$file\n"
+ exit 1
+endif
+
+# convert Wiggle ascii data file to binary format
+wigEncode $file test.$table.wig test.$table.wib
+
+# fetch wiggle data from table and perform stats
+hgWiggle -db=$db -doStats $table | grep -v '^#' > stats.$table.table
+
+# fetch wiggle data from file and perform stats
+hgWiggle -doStats test.$table.wig | grep -v '^#' > stats.$table.file
+
+# compare output files from two hgWiggle steps above
+diff -q stats.$table.file stats.$table.table
+
+if ( "F" != $remove ) then
+ rm -f test.$table.wig test.$table.wib stats.$table.*
+endif
+
+exit 0