From 6550be33502ed0379d8a4cec23382e8df293de52 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 19 Nov 2021 07:51:13 +0000
Subject: [PATCH] added info re having run mcsm_na for RNAP

---
 mcsm_na/split_csv.sh | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100755 mcsm_na/split_csv.sh

diff --git a/mcsm_na/split_csv.sh b/mcsm_na/split_csv.sh
new file mode 100755
index 0000000..89ccd6d
--- /dev/null
+++ b/mcsm_na/split_csv.sh
@@ -0,0 +1,27 @@
+#!/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_
+
+# use case
+#~/git/LSHTM_analysis/mcsm_na/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50
+#~/git/LSHTM_analysis/mcsm_na/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50
+
+
+#~/git/LSHTM_analysis/mcsm_na/split_csv.sh rpob_mcsm_formatted_snps_chain.csv snp_batches 20 # date: 17/11/2021
+
+
+#acccidently replaced file original rpob batches
+
+#~/git/LSHTM_analysis/mcsm_na/split_csv.sh 5uhc_mcsm_formatted_snps_chain.csv snp_batches_5uhc 20 # date: 17/11/2021