24 lines
852 B
Bash
Executable file
24 lines
852 B
Bash
Executable file
#!/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
|
|
|
|
INFILE=$1
|
|
OUTDIR=$2
|
|
CHUNK=$3
|
|
|
|
mkdir -p ${OUTDIR}/${CHUNK}
|
|
cd ${OUTDIR}/${CHUNK}
|
|
|
|
# makes the 2 dirs, hence ../..
|
|
split ../../${INFILE} -l ${CHUNK} -d snp_batch_
|
|
|
|
# use case
|
|
#~/git/LSHTM_analysis/dynamut/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50
|
|
#~/git/LSHTM_analysis/dynamut/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50
|
|
#~/git/LSHTM_analysis/dynamut/split_csv.sh pnca_mcsm_formatted_snps.csv snp_batches 50
|
|
#~/git/LSHTM_analysis/dynamut/split_csv.sh katg_mcsm_formatted_snps.csv snp_batches 50 #Date: 20/09/2021
|
|
|
|
# add .txt to the files
|