26 lines
737 B
Bash
Executable file
26 lines
737 B
Bash
Executable file
#!/bin/sh
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drug="pyrazinamide"
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gene="pnca"
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aa_python="/home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py"
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snp_dir="/home/tanu/git/Data/${drug}"
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aa_outfile="/home/tanu/git/Data/${drug}/output/aa_index/${gene}_aa"
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for i in $(cat ${snp_dir}/output/*mcsm_snps*)
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do
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echo -n "${i}," >> $aa_outfile
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python $aa_python $snp_dir/input/pnca_complex.pdb A $i >> $aa_outfile
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done
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# How I want it to run
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#gene = "pncA" # force it to be lowercase
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#chain = "A"
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#mutfile = "/home/tanu/git/Data/output/<gene>_mcsm_snps.csv"
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#mut = for i in mutfile
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#$1 = "/home/tanu/git/Data/input/<gene>_complex.pdb
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#$2 = chain
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#$3 = mut
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#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py $1 $2 $3
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