#!/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