22 lines
703 B
Bash
Executable file
22 lines
703 B
Bash
Executable file
#!/bin/bash
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# FIXME: This is written for expediency to kickstart running dynamut, mcsm-PPI2 (batch pf 50) and mCSM-NA (batch of 20)
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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 dynamut dir
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# use sed to add chain ID to snp file and then split to avoid post processing
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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}/chain_added
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cd ${OUTDIR}/${CHUNK}/chain_added
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# makes the 2 dirs, hence ../..
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split ../../../${INFILE} -l ${CHUNK} -d snp_batch_
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# use case
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#~/git/LSHTM_analysis/dynamut/split_csv_chain.sh katg_mcsm_formatted_snps.csv snp_batches 50 #Date: 20/09/2021
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# add .txt to the files
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