# HG changeset patch
# User davidvanzessen
# Date 1428584339 14400
# Node ID 2a7343e4be5a91376e607d9c9862461aebaa2fb7
# Parent  c623690e3b81f5657df398156a209c035395c83c
Uploaded

diff -r c623690e3b81 -r 2a7343e4be5a mutation_analysis.py
--- a/mutation_analysis.py	Thu Apr 09 08:52:18 2015 -0400
+++ b/mutation_analysis.py	Thu Apr 09 08:58:59 2015 -0400
@@ -11,6 +11,7 @@
 
 infile = args.input
 genes = str(args.genes).split(",")
+print "includefr1 =", args.includefr1
 include_fr1 = True if args.includefr1 == "yes" else False
 outfile = args.output 
 
diff -r c623690e3b81 -r 2a7343e4be5a wrapper.sh
--- a/wrapper.sh	Thu Apr 09 08:52:18 2015 -0400
+++ b/wrapper.sh	Thu Apr 09 08:58:59 2015 -0400
@@ -46,7 +46,7 @@
 echo "R mutation analysis"
 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
 echo "python mutation analysis"
-python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${inlcude_fr1}" --output $outdir/hotspot_analysis.txt
+python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
 echo "R AA histogram"
 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1