added separate script for splitting csv after adding chain ID. saves lots of post processing

dynamut/split_csv_chain.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# FIXME: This is written for expediency to kickstart running dynamut, mcsm-PPI2 (batch pf 50) and mCSM-NA (batch of 20)
+
+# 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
+# use sed to add chain ID to snp file and then split to avoid post processing
+
+INFILE=$1
+OUTDIR=$2
+CHUNK=$3
+
+mkdir -p ${OUTDIR}/${CHUNK}/chain_added
+cd ${OUTDIR}/${CHUNK}/chain_added
+
+# makes the 2 dirs, hence ../..
+split ../../../${INFILE} -l ${CHUNK} -d snp_batch_
+
+# use case
+#~/git/LSHTM_analysis/dynamut/split_csv_chain.sh katg_mcsm_formatted_snps.csv snp_batches 50     #Date: 20/09/2021
+
+# add .txt to the files