Mercurial > repos > davidvanzessen > mutation_analysis

changeset 32:2a7343e4be5a draft

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Uploaded
author davidvanzessen
date Thu, 09 Apr 2015 08:58:59 -0400
parents c623690e3b81
children ac9a4307861a
files mutation_analysis.py wrapper.sh
diffstat 2 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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 
 
--- 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