src/utils/qa/getChainLines.csh 1.1

Index: src/utils/qa/getChainLines.csh
===================================================================
RCS file: src/utils/qa/getChainLines.csh
diff -N src/utils/qa/getChainLines.csh
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/utils/qa/getChainLines.csh	23 Sep 2009 17:55:29 -0000	1.1
@@ -0,0 +1,72 @@
+#!/bin/tcsh
+source `which qaConfig.csh`
+
+
+###############################################
+# 
+#  09-23-2009
+#  Gets the two variables needed for chain blocks in trackDb.ra files.
+#  Written by Ann Zweig
+# 
+###############################################
+
+
+set db1=""
+set db2=""
+set out1=""
+set out2=""
+set chainMinScore=""
+set chainLinearGap=""
+set fullLine=""
+
+if ( $#argv != 2 ) then
+  echo
+  echo '  Searches the documentation to find the correct parameters for the '
+  echo '  $chainMinScore and $chainLinearGap variables. ' 
+  echo
+  echo '    usage:  fromDb toDb (these can be in either order)'
+  echo
+  exit
+else
+  set db1=$argv[1]
+  set db2=$argv[2]
+endif
+
+if ( "$HOST" != "hgwdev" ) then
+  echo "\n ERROR: you must run this script on dev!\n"
+  exit 1
+endif
+
+set Db1=`echo $db1 | perl -wpe '$_ = ucfirst($_)'`
+set Db2=`echo $db2 | perl -wpe '$_ = ucfirst($_)'`
+
+set out1=`grep -s "Chain minimum score" /data/apache/htdocs/goldenPath/$db1/vs$Db2/README.txt`
+set out2=`grep -s "Chain minimum score" /data/apache/htdocs/goldenPath/$db2/vs$Db1/README.txt`
+
+if ( "$out1" != "") then
+  set fullLine="$out1"
+else 
+  if ( "$out2" != "") then
+    set fullLine="$out2"
+  else
+    echo ' \nERROR: cannot find either $chain variable for this pair\n'
+    exit 1
+  endif
+endif
+
+# strip any white space from start and end of line
+set fullLine=`echo $fullLine | sed -e "s/^\s+//"`
+set fullLine=`echo $fullLine | sed -e "s/\z//"`
+
+if ( "$fullLine" != "" ) then
+  # extract the chainMinScore value
+  set minScore=`echo $fullLine | sed -e "s/Chain minimum score: //" \
+  | awk '{print $1}' | sed -e "s/,//"`
+  echo '$chainMinScore '$minScore
+  
+  # extract the chainLinearGap method
+  set linearGap=`echo $fullLine | awk '{print $9}' | sed "s/://" \
+  | sed "s/(//" | sed "s/)//"`
+  echo '$chainLinearGap '$linearGap
+
+exit