Coverage for biobb_pdb_tools/pdb_tools/biobb_pdb_seg.py: 78%

1#!/usr/bin/env python3 

2 

3"""Module containing the Pdbseg class and the command line interface.""" 

4 

5import argparse 

6from typing import Optional 

7 

8from biobb_common.configuration import settings 

9from biobb_common.generic.biobb_object import BiobbObject 

10from biobb_common.tools import file_utils as fu 

11from biobb_common.tools.file_utils import launchlogger 

12 

13 

14# 1. Rename class as required 

15class Pdbseg(BiobbObject): 

16 """ 

17 | biobb_pdb_tools Pdbseg 

18 | Modifies the segment identifier column of a PDB file. 

19 | This tool modifies the segment identifier column of a PDB file. It can be used to change the segment identifier of a PDB file or to remove the segment identifier from a PDB file. 

20 

21 Args: 

22 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_seg.pdb>`_. Accepted formats: pdb (edam:format_1476). 

23 output_file_path (str): PDB file with segment identifier column modified. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_seg.pdb>`_. Accepted formats: pdb (edam:format_1476). 

24 properties (dic): 

25 * **segment** (*str*) - ('B') Default is an empty segment. 

26 * **binary_path** (*str*) - ("pdb_seg") Path to the pdb_seg executable binary. 

27 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. 

28 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. 

29 

30 Examples: 

31 This is a use example of how to use the building block from Python:: 

32 

33 from biobb_pdb_tools.pdb_tools.biobb_pdb_seg import biobb_pdb_seg 

34 

35 prop = { 

36 'segment': 'A' 

37 } 

38 biobb_pdb_seg(input_file_path='/path/to/input.pdb', 

39 output_file_path='/path/to/output.pdb', 

40 properties=prop) 

41 

42 Info: 

43 * wrapped_software: 

44 * name: pdb_tools 

45 * version: >=2.5.0 

46 * license: Apache-2.0 

47 * ontology: 

48 * name: EDAM 

49 * schema: http://edamontology.org/EDAM.owl 

50 

51 """ 

52 

53 def __init__( 

54 self, input_file_path, output_file_path, properties=None, **kwargs 

55 ) -> None: 

56 properties = properties or {} 

57 super().__init__(properties) 

58 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 } 

63 

64 self.binary_path = properties.get("binary_path", "pdb_seg") 

65 self.segment = properties.get("segment", False) 

66 self.properties = properties 

67 

68 self.check_properties(properties) 

69 self.check_arguments() 

70 

71 @launchlogger 

72 def launch(self) -> int: 

73 """Execute the :class:`Pdbseg <biobb_pdb_tools.pdb_tools.pdb_seg>` object.""" 

74 

75 if self.check_restart(): 

76 return 0 

77 self.stage_files() 

78 

79 instructions = [] 

80 if self.segment: 

81 instructions.append("-" + str(self.segment)) 

82 fu.log("Appending optional boolean property", self.out_log, self.global_log) 

83 

84 self.cmd = [ 

85 self.binary_path, 

86 " ".join(instructions), 

87 self.stage_io_dict["in"]["input_file_path"], 

88 ">", 

89 self.io_dict["out"]["output_file_path"], 

90 ] 

91 

92 fu.log(" ".join(self.cmd), self.out_log, self.global_log) 

93 

94 fu.log( 

95 "Creating command line with instructions and required arguments", 

96 self.out_log, 

97 self.global_log, 

98 ) 

99 self.run_biobb() 

100 self.copy_to_host() 

101 

102 self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) 

103 self.remove_tmp_files() 

104 self.check_arguments(output_files_created=True, raise_exception=False) 

105 

106 return self.return_code 

107 

108 

109def biobb_pdb_seg( 

110 input_file_path: str, 

111 output_file_path: str, 

112 properties: Optional[dict] = None, 

113 **kwargs, 

114) -> int: 

115 """Create :class:`Pdbseg <biobb_pdb_tools.pdb_tools.pdb_seg>` class and 

116 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_seg.launch>` method.""" 

117 

118 return Pdbseg( 

119 input_file_path=input_file_path, 

120 output_file_path=output_file_path, 

121 properties=properties, 

122 **kwargs, 

123 ).launch() 

124 

125biobb_pdb_seg.__doc__ = Pdbseg.__doc__ 

126 

127 

128def main(): 

129 """Command line execution of this building block. Please check the command line documentation.""" 

130 parser = argparse.ArgumentParser( 

131 description="Modifies the segment identifier column of a PDB file.", 

132 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999), 

133 ) 

134 parser.add_argument("--config", required=True, help="Configuration file") 

135 

136 required_args = parser.add_argument_group("required arguments") 

137 required_args.add_argument( 

138 "--input_file_path", 

139 required=True, 

140 help="Description for the first input file path. Accepted formats: pdb.", 

141 ) 

142 required_args.add_argument( 

143 "--output_file_path", 

144 required=True, 

145 help="Description for the output file path. Accepted formats: pdb.", 

146 ) 

147 

148 args = parser.parse_args() 

149 args.config = args.config or "{}" 

150 properties = settings.ConfReader(config=args.config).get_prop_dic() 

151 

152 biobb_pdb_seg( 

153 input_file_path=args.input_file_path, 

154 output_file_path=args.output_file_path, 

155 properties=properties, 

156 ) 

157 

158 

159if __name__ == "__main__": 

160 main()