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saving work for logo plots

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Tanushree Tunstall 2022-01-13 18:53:47 +00:00
parent 7cbd9b4996
commit 344a74a9e1
5 changed files with 24 additions and 29 deletions
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19
scripts/run_mutate.sh
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@ -15,3 +15,22 @@ python3 mutate.py -v -o /home/tanu/git/Data/pyrazinamide/output/pnca_msa.txt /ho
sed -i '/^>.*$/d' /home/tanu/git/Data/pyrazinamide/output/pnca_msa.txt
printf 'No. of lines after cleaning: '
cat /home/tanu/git/Data/pyrazinamide/output/pnca_msa.txt | wc -l
#%%
# Date: 13/01/22
# pre processing
sed 's/"//g' gene_msa_snp.csv > gid_mut_map.csv
# mut prefix for mutation map file MUST match fasta file header
python3 mutate.py -v -o /home/tanu/git/LSHTM_analysis/scripts/plotting/scratch_plots/TEST2.csv /home/tanu/git/LSHTM_analysis/scripts/plotting/scratch_plots/gid_mut_map.csv /home/tanu/git/Data/streptomycin/input/gid2.fasta
wc -l TEST2.csv
# post processing
sed -E 's/>.*//g' TEST2.csv | sed '/^$/d' > TEST3.csv
wc -l TEST3.csv
# doubles the no as it adds the mut info
python3 mutate.py -v -o /home/tanu/git/LSHTM_analysis/scripts/plotting/scratch_plots/TEST.csv /home/tanu/git/LSHTM_analysis/scripts/plotting/scratch_plots/pnca_mut_map.csv /home/tanu/git/Data/pyrazinamide/input/pnca.fasta