added split_csv.sh

dynamut/split_csv.sh

@@ -0,0 +1,18 @@
+#!/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 dynamut dir
+
+INFILE=$1
+OUTDIR=$2
+CHUNK=$3
+
+mkdir -p ${OUTDIR}/${CHUNK}
+cd ${OUTDIR}/${CHUNK}
+
+split ../../${INFILE} -l ${CHUNK} -d snp_batch_
+
+# use case
+#~/git/LSHTM_analysis/dynamut/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50