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added cmd option for dynamut2 formatting results

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This commit is contained in:
Tanushree Tunstall 2021-10-18 13:52:29 +01:00
parent c5c4d74acf
commit a67a07db2d
7 changed files with 65 additions and 16 deletions
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21
dynamut/split_csv_chain.sh
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@ -13,10 +13,25 @@ CHUNK=$3
mkdir -p ${OUTDIR}/${CHUNK}/chain_added
cd ${OUTDIR}/${CHUNK}/chain_added
# makes the 2 dirs, hence ../..
# makes the 3 dirs, hence ../..
split ../../../${INFILE} -l ${CHUNK} -d snp_batch_
# use case
#~/git/LSHTM_analysis/dynamut/split_csv_chain.sh katg_mcsm_formatted_snps.csv snp_batches 50 #Date: 20/09/2021
########################################################################
# 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
########################################################################