b9fced4a76dc41a844370d987ed5121a9966e93c rhead Thu Apr 14 11:47:11 2011 -0700 Changed usage statement to be slightly more specific. diff --git src/utils/qa/getChainLines.csh src/utils/qa/getChainLines.csh index b0e5a9e..d5074a9 100755 --- src/utils/qa/getChainLines.csh +++ src/utils/qa/getChainLines.csh @@ -1,72 +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 ' Searches the README.txt files 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($_)'` set out1=`grep -s "Chain minimum score" /data/apache/htdocs-hgdownload/goldenPath/$db1/vs$Db2/README.txt` set out2=`grep -s "Chain minimum score" /data/apache/htdocs-hgdownload/goldenPath/$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