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added info re having run mcsm_na for RNAP

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Tanushree Tunstall 2021-11-19 07:51:13 +00:00
parent 7fd5e2710d
commit 6550be3350
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mcsm_na/split_csv.sh Executable file
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#!/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