#!/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 3 dirs, hence ../..
split ../../../${INFILE} -l ${CHUNK} -d snp_batch_

########################################################################
# use cases
# Date: 20/09/2021
# sed -e 's/^/A /g' katg_mcsm_formatted_snps.csv > katg_mcsm_formatted_snps_chain.csv
#~/git/LSHTM_analysis/dynamut/split_csv_chain.sh katg_mcsm_formatted_snps_chain.csv snp_batches 50

# Date: 01/10/2021
# sed -e 's/^/A /g' rpob_mcsm_formatted_snps.csv > rpob_mcsm_formatted_snps_chain.csv
#~/git/LSHTM_analysis/dynamut/split_csv_chain.sh rpob_mcsm_formatted_snps_chain.csv snp_batches 50     

# Date: 02/10/2021
# sed -e 's/^/A /g' alr_mcsm_formatted_snps.csv > alr_mcsm_formatted_snps_chain.csv
#~/git/LSHTM_analysis/dynamut/split_csv_chain.sh alr_mcsm_formatted_snps_chain.csv snp_batches 50  

# Date: 05/10/2021
#~/git/LSHTM_analysis/dynamut/split_csv_chain.sh alr_mcsm_formatted_snps_chain.csv snp_batches 20    
  
# add .txt to the files
########################################################################