#!/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