# HG changeset patch
# User davidvanzessen
# Date 1466166680 14400
# Node ID 3cffb8a38bb1116d09d0f991246f30333cc9bc98
# Parent  ff5be711382b2cabb5b6df9ba2e10cf441786da5
Uploaded

diff -r ff5be711382b -r 3cffb8a38bb1 tmp/igat.r
--- a/tmp/igat.r	Fri Jun 17 05:36:32 2016 -0400
+++ b/tmp/igat.r	Fri Jun 17 08:31:20 2016 -0400
@@ -6,6 +6,8 @@
 
 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
 
+print(head(merged$best_match))
+
 if(gene != "-"){
 	merged = merged[grepl(gene, merged$best_match),]
 }
diff -r ff5be711382b -r 3cffb8a38bb1 wrapper.sh
--- a/wrapper.sh	Fri Jun 17 05:36:32 2016 -0400
+++ b/wrapper.sh	Fri Jun 17 08:31:20 2016 -0400
@@ -103,9 +103,9 @@
 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
 
 Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
-Rscript $dir/tmp/igat.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca "2>&1
-Rscript $dir/tmp/igat.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg "2>&1
-Rscript $dir/tmp/igat.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm "2>&1
+Rscript $dir/tmp/igat.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1
+Rscript $dir/tmp/igat.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1
+Rscript $dir/tmp/igat.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1
 
 
 tmp="$PWD"
@@ -297,11 +297,29 @@
 echo "</html>" >> $output
 
 echo "---------------- baseline ----------------"
+tmp="$PWD"
+
+mkdir $outdir/baseline
+
+
+mkdir $outdir/baseline/ca_cg_cm
+cd $outdir/baseline/ca_cg_cm
 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
+
+mkdir $outdir/baseline/ca
+cd $outdir/baseline/ca
 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt"
+
+mkdir $outdir/baseline/cg
+cd $outdir/baseline/cg
 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt"
+
+mkdir $outdir/baseline/cm
+cd $outdir/baseline/cm
 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt"
 
+cd $tmp
+
 #optional output for naive
 
 echo "---------------- naive_output.r ----------------"