27 lines
843 B
Bash
Executable file
27 lines
843 B
Bash
Executable file
#!/bin/bash
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# FIXME: This is written for expediency to kickstart running dynamut and mcsm-NA
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# Usage: ~/git/LSHTM_analysis/dynamut/split_csv.sh <input file> <output dir> <chunk size in lines>
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# copy your snp file to split into the mcsm_na dir
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INFILE=$1
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OUTDIR=$2
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CHUNK=$3
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mkdir -p ${OUTDIR}/${CHUNK}
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cd ${OUTDIR}/${CHUNK}
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split ../../${INFILE} -l ${CHUNK} -d snp_batch_
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# use case
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#~/git/LSHTM_analysis/mcsm_na/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50
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#~/git/LSHTM_analysis/mcsm_na/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50
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#~/git/LSHTM_analysis/mcsm_na/split_csv.sh rpob_mcsm_formatted_snps_chain.csv snp_batches 20 # date: 17/11/2021
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#acccidently replaced file original rpob batches
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#~/git/LSHTM_analysis/mcsm_na/split_csv.sh 5uhc_mcsm_formatted_snps_chain.csv snp_batches_5uhc 20 # date: 17/11/2021
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