Mercurial > repos > davidvanzessen > argalaxy_tools

diff report_clonality/r_wrapper.sh @ 22:c28da767799f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Fri, 27 Jan 2017 04:24:41 -0500
parents 3ef457aa5df6
children e2fbdfacec1d
line wrap: on
line diff
--- a/report_clonality/r_wrapper.sh	Fri Jan 27 03:58:45 2017 -0500
+++ b/report_clonality/r_wrapper.sh	Fri Jan 27 04:24:41 2017 -0500
@@ -258,14 +258,14 @@
 			echo "</table></div>" >> $outputFile
 		else
 			echo "in new"
-			clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)"
+			clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)"
 			echo "<div class='tabbertab' title='$sample'>" >> $outputFile
 			echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile
 			echo "<table border = 1>" >> $outputFile
 			while IFS=, read type count
 			do
 				echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
-			done < $outputDir/lymphclon_coincidences_$sample.csv
+			done < $outputDir/lymphclon_coincidences_$sample.txt
 			echo "</table></div>" >> $outputFile
 		fi
 	done