Coverage for biobb_pdb_tools/pdb_tools/biobb_pdb_splitseg.py: 74%
62 statements
« prev ^ index » next coverage.py v7.9.1, created at 2025-06-20 08:28 +0000
1#!/usr/bin/env python3
3"""Module containing the Pdbsplitseg class and the command line interface."""
5import argparse
6import glob
7import os
8import zipfile
9from pathlib import Path
10from typing import Optional
12from biobb_common.configuration import settings
13from biobb_common.generic.biobb_object import BiobbObject
14from biobb_common.tools import file_utils as fu
15from biobb_common.tools.file_utils import launchlogger
18class Pdbsplitseg(BiobbObject):
19 """
20 | biobb_pdb_tools Pdbsplitseg
21 | Splits a PDB file into several, each containing one segment.
22 | This tool splits a PDB file into several, each containing one segment. It can be used to split a PDB file into several, each containing one segment.
24 Args:
25 input_file_path (str): PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/input_pdb_splitseg.pdb>`_. Accepted formats: pdb (edam:format_1476).
26 output_file_path (str): ZIP file containing all PDB files splited by protein segment. File type: output. `Sample file <https://github.com/bioexcel/biobb_pdb_tools/blob/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_splitseg.zip>`_. Accepted formats: zip (edam:format_3987).
27 properties (dic):
28 * **binary_path** (*str*) - ("pdb_splitseg") Path to the pdb_splitseg executable binary.
29 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
30 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
32 Examples:
33 This is a use example of how to use the building block from Python::
35 from biobb_pdb_tools.pdb_tools.biobb_pdb_splitseg import biobb_pdb_splitseg
37 biobb_pdb_splitseg(input_file_path='/path/to/input.pdb',
38 output_file_path='/path/to/output.pdb')
40 Info:
41 * wrapped_software:
42 * name: pdb_tools
43 * version: >=2.5.0
44 * license: Apache-2.0
45 * ontology:
46 * name: EDAM
47 * schema: http://edamontology.org/EDAM.owl
49 """
51 def __init__(
52 self, input_file_path, output_file_path, properties=None, **kwargs
53 ) -> None:
54 properties = properties or {}
56 super().__init__(properties)
57 self.locals_var_dict = locals().copy()
59 self.io_dict = {
60 "in": {"input_file_path": input_file_path},
61 "out": {"output_file_path": output_file_path},
62 }
64 self.binary_path = properties.get("binary_path", "pdb_splitseg")
65 self.properties = properties
67 self.check_properties(properties)
68 self.check_arguments()
70 @launchlogger
71 def launch(self) -> int:
72 """Execute the :class:`Pdbsplitseg <biobb_pdb_tools.pdb_tools.pdb_splitseg>` object."""
74 if self.check_restart():
75 return 0
76 self.stage_files()
78 self.cmd = [
79 "cd",
80 self.stage_io_dict.get("unique_dir", ""),
81 ";",
82 self.binary_path,
83 self.stage_io_dict["in"]["input_file_path"],
84 ]
86 fu.log(" ".join(self.cmd), self.out_log, self.global_log)
87 fu.log(
88 "Creating command line with instructions and required arguments",
89 self.out_log,
90 self.global_log,
91 )
92 self.run_biobb()
94 stem = Path(self.stage_io_dict["in"]["input_file_path"]).stem
95 pdb_files = glob.glob(
96 os.path.join(self.stage_io_dict.get(
97 "unique_dir", ""), stem + "_*.pdb")
98 )
100 if len(pdb_files) > 1:
101 output_zip_path = os.path.join(
102 self.stage_io_dict.get("unique_dir", ""),
103 self.stage_io_dict["out"]["output_file_path"],
104 )
105 fu.log(
106 "Saving %d pdb segment files in a zip" % len(pdb_files),
107 self.out_log,
108 self.global_log,
109 )
110 with zipfile.ZipFile(output_zip_path, "w") as zipf:
111 for pdb_file in pdb_files:
112 zipf.write(pdb_file, os.path.basename(pdb_file))
113 else:
114 fu.log(
115 "The given input file has no segments. Saving the input file into a zip.",
116 self.out_log,
117 self.global_log,
118 )
119 output_zip_path = os.path.join(
120 self.stage_io_dict.get("unique_dir", ""),
121 self.stage_io_dict["out"]["output_file_path"],
122 )
123 with zipfile.ZipFile(output_zip_path, "w") as zipf:
124 zipf.write(
125 self.stage_io_dict["in"]["input_file_path"],
126 os.path.basename(
127 self.stage_io_dict["in"]["input_file_path"]),
128 )
129 pass
131 self.copy_to_host()
132 self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
133 self.remove_tmp_files()
134 self.check_arguments(output_files_created=True, raise_exception=False)
136 return self.return_code
139def biobb_pdb_splitseg(
140 input_file_path: str,
141 output_file_path: str,
142 properties: Optional[dict] = None,
143 **kwargs,
144) -> int:
145 """Create :class:`Pdbsplitseg <biobb_pdb_tools.pdb_tools.pdb_splitseg>` class and
146 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_splitseg.launch>` method."""
148 return Pdbsplitseg(
149 input_file_path=input_file_path,
150 output_file_path=output_file_path,
151 properties=properties,
152 **kwargs,
153 ).launch()
156biobb_pdb_splitseg.__doc__ = Pdbsplitseg.__doc__
159def main():
160 """Command line execution of this building block. Please check the command line documentation."""
161 parser = argparse.ArgumentParser(
162 description="Splits a PDB file into several, each containing one segment.",
163 formatter_class=lambda prog: argparse.RawTextHelpFormatter(
164 prog, width=99999),
165 )
166 parser.add_argument("--config", required=True, help="Configuration file")
168 required_args = parser.add_argument_group("required arguments")
169 required_args.add_argument(
170 "--input_file_path",
171 required=True,
172 help="Description for the input file path. Accepted formats: pdb.",
173 )
174 required_args.add_argument(
175 "--output_file_path",
176 required=True,
177 help="Description for the output file path. Accepted formats: zip.",
178 )
180 args = parser.parse_args()
181 args.config = args.config or "{}"
182 properties = settings.ConfReader(config=args.config).get_prop_dic()
184 biobb_pdb_splitseg(
185 input_file_path=args.input_file_path,
186 output_file_path=args.output_file_path,
187 properties=properties,
188 )
191if __name__ == "__main__":
192 main()