added shell script to format muts for mcsm NA

mcsm_na/split_format_csv.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# FIXME: This is written for expediency to kickstart running dynamut and mcsm-NA
+
+# Usage: ~/git/LSHTM_analysis/dynamut/split_csv.sh <input file> <output dir> <chunk size in lines>
+# copy your snp file to split into the mcsm_na dir
+
+INFILE=$1
+OUTDIR=$2
+CHUNK=$3
+
+mkdir -p ${OUTDIR}/${CHUNK}
+cd ${OUTDIR}/${CHUNK}
+
+split ../../${INFILE} -l ${CHUNK} -d snp_batch_
+for i in *; do mv $i $i.txt; done
+sed -i 's/^/A /g' *.txt
+
+