51 lines
1 KiB
Bash
Executable file
51 lines
1 KiB
Bash
Executable file
#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Sun Feb 16 11:21:44 2020
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@author: tanu
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"""
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#!/usr/bin/bash
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# Run dssp exe
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#%%
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# specify variables for input and output paths and filenames
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drug="pyrazinamide"
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#gene = "pnca"
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datadir="~git/Data"
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basedir=${datadir}"/"${drug}
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echo${basedir}
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# input
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inpath="/original"
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# uncomment as necessary
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in_filename="/3pl1.pdb"
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infile=${basedir}${inpath}${in_filename}
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echo${infile}
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# output file
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outpath="/processed"
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outdir=${datadir}"/"${drug}${outpath}
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out_filename="/3pl1.dssp"
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outfile=${outdir}${out_filename}
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echo${outdir}
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if not os.path.exists(datadir):
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print('Error!', datadir, 'does not exist. Please ensure it exists. Dir struc specified in README.md')
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os.makedirs(datadir)
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exit()
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if not os.path.exists(outdir):
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print('Error!', outdir, 'does not exist.Please ensure it exists. Dir struc specified in README.md')
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exit()
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else:
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print('Dir exists: Carrying on')
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# end of variable assignment for input and output files
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#%%
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# ommand line args
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dssp -i 3pl1.pdb -o 3pl1.dssp
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dssp -i
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