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", 

83 self.out_log, self.global_log) 

84 

85 self.cmd = [ 

86 self.binary_path, 

87 " ".join(instructions), 

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

89 ">", 

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

91 ] 

92 

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

94 

95 fu.log( 

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

97 self.out_log, 

98 self.global_log, 

99 ) 

100 self.run_biobb() 

101 self.copy_to_host() 

102 

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

104 self.remove_tmp_files() 

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

106 

107 return self.return_code 

108 

109 

110def biobb_pdb_seg( 

111 input_file_path: str, 

112 output_file_path: str, 

113 properties: Optional[dict] = None, 

114 **kwargs, 

115) -> int: 

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

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

118 

119 return Pdbseg( 

120 input_file_path=input_file_path, 

121 output_file_path=output_file_path, 

122 properties=properties, 

123 **kwargs, 

124 ).launch() 

125 

126 

127biobb_pdb_seg.__doc__ = Pdbseg.__doc__ 

128 

129 

130def main(): 

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

132 parser = argparse.ArgumentParser( 

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

134 formatter_class=lambda prog: argparse.RawTextHelpFormatter( 

135 prog, width=99999), 

136 ) 

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

138 

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

140 required_args.add_argument( 

141 "--input_file_path", 

142 required=True, 

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

144 ) 

145 required_args.add_argument( 

146 "--output_file_path", 

147 required=True, 

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

149 ) 

150 

151 args = parser.parse_args() 

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

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

154 

155 biobb_pdb_seg( 

156 input_file_path=args.input_file_path, 

157 output_file_path=args.output_file_path, 

158 properties=properties, 

159 ) 

160 

161 

162if __name__ == "__main__": 

163 main()