Mercurial > repos > davidvanzessen > mutation_analysis

diff wrapper.sh @ 31:c623690e3b81 draft

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author davidvanzessen
date Thu, 09 Apr 2015 08:52:18 -0400
parents 2433a1e110e1
children 2a7343e4be5a
line wrap: on
line diff
--- a/wrapper.sh	Thu Apr 09 07:59:06 2015 -0400
+++ b/wrapper.sh	Thu Apr 09 08:52:18 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 --output $outdir/hotspot_analysis.txt
+python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${inlcude_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