71 lines
2.5 KiB
Python
Executable file
71 lines
2.5 KiB
Python
Executable file
#!/usr/bin/env python3
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# Copyright 2020, Tanushree Tunstall
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# This program is distributed under General Public License v. 3. See the file
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# COPYING for a copy of the license.
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__description__ = \
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"""
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chain_splitter.py
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extract chain/s from pdb and saves each chain as a separate file
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"""
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__author__ = "Tanushree Tunstall"
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__date__ = ""
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#=======================================================================
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import os, shutil, sys
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#from pdbtools.helper import cmdline
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from chain_splitter import ChainSelect
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from Bio.PDB import Select, PDBIO
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from Bio.PDB.PDBParser import PDBParser
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#io = PDBIO()
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import argparse
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#=======================================================================
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def main():
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"""
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Function to call if run from command line.
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Example use:
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pdb_chain_splitter.py -f <your_pdb_file> -c <chainid1><chainid2>
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Extracts chain 'A' by default.
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FIXME: extract all chains from the given pdb and write them out individually
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"""
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arg_parser = argparse.ArgumentParser()
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arg_parser.add_argument('-i', '--pdb_file', help='provide pdb file', default = 'None')
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arg_parser.add_argument('-c', '--chain', help='chain/s to extract without spaces.', nargs = '+', default = 'A', type = list)
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arg_parser.add_argument('-p', '--out_path', help='specify output path', default = '.', type = str)
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arg_parser.add_argument('-o', '--out_file', help='specify output filename. Will be used as a prefix to append chain id and pdb file extension', default = 'pdb_file_chain', type = str)
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args = arg_parser.parse_args()
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# Extract chains and write each chain as a separate file
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pdb_file = args.pdb_file
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print('input pdb file:', pdb_file)
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# type = list, makes it a list of lists. Hence extracting the list of chains.
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chains = args.chain[0]
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#chains = ['A','B','C']
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print ('user supplied chain:', chains)
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# output filename and path
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outpath = args.out_path
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outfile = args.out_file
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# get structure
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p = PDBParser(PERMISSIVE=1)
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structure = p.get_structure(pdb_file, pdb_file)
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print('input pdb filename:', structure.get_id())
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for chain in chains:
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chain = chain.upper()
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print ('Extracting chain:', chain)
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pdb_chain_file = outpath + '/' + outfile + '_{}.pdb'.format(chain)
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io = PDBIO()
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io.set_structure(structure)
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io.save('{}'.format(pdb_chain_file), ChainSelect(chain))
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if __name__ == "__main__":
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main()
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