# HG changeset patch
# User davidvanzessen
# Date 1470831617 14400
# Node ID 4984c2a06c43f76b506bd2161b7700f5724f71fa
# Parent  ede6c4ee5196ea2e524edad33537ab23d9c2187d
Uploaded

diff -r ede6c4ee5196 -r 4984c2a06c43 mutation_analysis.r
diff -r ede6c4ee5196 -r 4984c2a06c43 wrapper.sh
--- a/wrapper.sh	Tue Aug 09 08:26:15 2016 -0400
+++ b/wrapper.sh	Wed Aug 10 08:20:17 2016 -0400
@@ -102,15 +102,42 @@
 mkdir $outdir/new_IMGT_ca
 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca
 
+mkdir $outdir/new_IMGT_ca1
+cp $outdir/new_IMGT/* $outdir/new_IMGT_ca1
+
+mkdir $outdir/new_IMGT_ca2
+cp $outdir/new_IMGT/* $outdir/new_IMGT_ca2
+
 mkdir $outdir/new_IMGT_cg
 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg
 
+mkdir $outdir/new_IMGT_cg1
+cp $outdir/new_IMGT/* $outdir/new_IMGT_cg1
+
+mkdir $outdir/new_IMGT_cg2
+cp $outdir/new_IMGT/* $outdir/new_IMGT_cg2
+
+mkdir $outdir/new_IMGT_cg3
+cp $outdir/new_IMGT/* $outdir/new_IMGT_cg3
+
+mkdir $outdir/new_IMGT_cg4
+cp $outdir/new_IMGT/* $outdir/new_IMGT_cg4
+
 mkdir $outdir/new_IMGT_cm
 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
 
 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
+
 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1
+Rscript $dir/new_imgt.r $outdir/new_IMGT_ca1/ $outdir/merged.txt "ca1" 2>&1
+Rscript $dir/new_imgt.r $outdir/new_IMGT_ca2/ $outdir/merged.txt "ca2" 2>&1
+
 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1
+Rscript $dir/new_imgt.r $outdir/new_IMGT_cg1/ $outdir/merged.txt "cg1" 2>&1
+Rscript $dir/new_imgt.r $outdir/new_IMGT_cg2/ $outdir/merged.txt "cg2" 2>&1
+Rscript $dir/new_imgt.r $outdir/new_IMGT_cg3/ $outdir/merged.txt "cg3" 2>&1
+Rscript $dir/new_imgt.r $outdir/new_IMGT_cg4/ $outdir/merged.txt "cg4" 2>&1
+
 Rscript $dir/new_imgt.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1
 
 
@@ -347,7 +374,13 @@
 #echo "<tr><td></td><td><a href='IgAT_cm.zip'>IgAT cm zip</a></td></tr>" >> $output
 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output
 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output
+echo "<tr><td>An IMGT archive with just the matched and filtered ca1 sequences</td><td><a href='new_IMGT_ca1.txz'>Download</a></td></tr>" >> $output
+echo "<tr><td>An IMGT archive with just the matched and filtered ca2 sequences</td><td><a href='new_IMGT_ca2.txz'>Download</a></td></tr>" >> $output
 echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz'>Download</a></td></tr>" >> $output
+echo "<tr><td>An IMGT archive with just the matched and filtered cg1 sequences</td><td><a href='new_IMGT_cg1.txz'>Download</a></td></tr>" >> $output
+echo "<tr><td>An IMGT archive with just the matched and filtered cg2 sequences</td><td><a href='new_IMGT_cg2.txz'>Download</a></td></tr>" >> $output
+echo "<tr><td>An IMGT archive with just the matched and filtered cg3 sequences</td><td><a href='new_IMGT_cg3.txz'>Download</a></td></tr>" >> $output
+echo "<tr><td>An IMGT archive with just the matched and filtered cg4 sequences</td><td><a href='new_IMGT_cg4.txz'>Download</a></td></tr>" >> $output
 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</a></td></tr>" >> $output
 echo "</table>" >> $output