18 lines
1 KiB
Bash
Executable file
18 lines
1 KiB
Bash
Executable file
#!/bin/bash
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#https://www.biostars.org/p/336891/
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#python Mutate.py -v -o /path/to/output.fasta mutation_map_file.csv input.fasta
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# pnca_all_muts_msa_FIXME: This should be formatted like this from python script
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# change to a cmd script that takes this "prefix" as an input
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for i in $(cat pnca_all_muts_msa_FIXME.csv); do echo "3PL1,${i}"; done > pnca_copy.txt
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# make sure there is no new line at the end of the mutation file (snps.csv)
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#python3 Mutate.py -v -o /home/tanu/git/Data/pyrazinamide/input/output.fasta mut_map.csv 3pl1.fasta.txt
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python3 mutate.py -v -o /home/tanu/git/Data/pyrazinamide/output/pnca_msa.txt /home/tanu/git/Data/pyrazinamide/output/pnca_all_muts_msa.csv /home/tanu/git/Data/pyrazinamide/input/pnca_fasta.txt
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# remove fasta style header lines in the output i.e
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# lines beginning with '>' so the file is just the mutated seqs
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sed -i '/^>.*$/d' /home/tanu/git/Data/pyrazinamide/output/pnca_msa.txt
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printf 'No. of lines after cleaning: '
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cat /home/tanu/git/Data/pyrazinamide/output/pnca_msa.txt | wc -l
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