Coverage for biobb_pdb_tools/pdb_tools/biobb_pdb_merge.py: 80%

1#!/usr/bin/env python3 

2 

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

4 

5import argparse 

6import os 

7import zipfile 

8from pathlib import Path 

9from typing import Optional 

10 

11from biobb_common.configuration import settings 

12from biobb_common.generic.biobb_object import BiobbObject 

13from biobb_common.tools import file_utils as fu 

14from biobb_common.tools.file_utils import launchlogger 

15 

16 

17class Pdbmerge(BiobbObject): 

18 """ 

19 | biobb_pdb_tools Pdbmerge 

20 | Merges several PDB files into one. 

21 | This tool merges several PDB files into one. It can be used to merge several PDB files into one. 

22 

23 Args: 

24 input_file_path (str): ZIP file of selected protein. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/input_pdb_merge.pdb>`_. Accepted formats: zip (edam:format_3987). 

25 output_file_path (str): PDB file with input PDBs merged. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_merge.pdb>`_. Accepted formats: pdb (edam:format_1476). 

26 properties (dic): 

27 * **binary_path** (*str*) - ("pdb_merge") Path to the pdb_merge executable binary. 

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

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

30 

31 Examples: 

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

33 

34 from biobb_pdb_tools.pdb_tools.biobb_pdb_merge import biobb_pdb_merge 

35 

36 biobb_pdb_merge(input_file_path='/path/to/input1.zip', 

37 output_file_path='/path/to/output.pdb') 

38 

39 Info: 

40 * wrapped_software: 

41 * name: pdb_tools 

42 * version: >=2.5.0 

43 * license: Apache-2.0 

44 * ontology: 

45 * name: EDAM 

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

47 

48 """ 

49 

50 def __init__( 

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

52 ) -> None: 

53 properties = properties or {} 

54 

55 super().__init__(properties) 

56 self.locals_var_dict = locals().copy() 

57 

58 self.io_dict = { 

59 "in": {"input_file_path": input_file_path}, 

60 "out": {"output_file_path": output_file_path}, 

61 } 

62 

63 self.binary_path = properties.get("binary_path", "pdb_merge") 

64 self.properties = properties 

65 

66 self.check_properties(properties) 

67 self.check_arguments() 

68 

69 @launchlogger 

70 def launch(self) -> int: 

71 """Execute the :class:`Pdbmerge <biobb_pdb_tools.pdb_tools.pdb_merge>` object.""" 

72 

73 if self.check_restart(): 

74 return 0 

75 self.stage_files() 

76 

77 input_file_path = self.stage_io_dict["in"]["input_file_path"] 

78 folder_path = os.path.dirname(input_file_path) 

79 

80 if zipfile.is_zipfile(input_file_path): 

81 with zipfile.ZipFile(input_file_path, "r") as zip_ref: 

82 zip_ref.extractall(folder_path) 

83 

84 pdb_files = [ 

85 file 

86 for file in os.listdir(folder_path) 

87 if file.lower().endswith(".pdb") 

88 ] 

89 

90 input_file_list = [os.path.join(folder_path, file) for file in pdb_files] 

91 

92 input_file_list = [Path(i) for i in input_file_list] 

93 input_file_list = sorted(input_file_list, key=lambda i: i.stem.upper()) 

94 input_file_list = [str(i) for i in input_file_list] 

95 

96 self.cmd = [ 

97 self.binary_path, 

98 *input_file_list, 

99 ">", 

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

101 ] 

102 

103 else: 

104 fu.log( 

105 f"The archive {input_file_path} is not a ZIP!", 

106 self.out_log, 

107 self.global_log, 

108 ) 

109 

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

111 

112 fu.log( 

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

114 self.out_log, 

115 self.global_log, 

116 ) 

117 

118 self.run_biobb() 

119 self.copy_to_host() 

120 

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

122 self.remove_tmp_files() 

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

124 

125 return self.return_code 

126 

127 

128def biobb_pdb_merge( 

129 input_file_path: str, 

130 output_file_path: str, 

131 properties: Optional[dict] = None, 

132 **kwargs, 

133) -> int: 

134 """Create :class:`Pdbmerge <biobb_pdb_tools.pdb_tools.pdb_merge>` class and 

135 execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_merge.launch>` method.""" 

136 return Pdbmerge( 

137 input_file_path=input_file_path, 

138 output_file_path=output_file_path, 

139 properties=properties, 

140 **kwargs, 

141 ).launch() 

142 

143biobb_pdb_merge.__doc__ = Pdbmerge.__doc__ 

144 

145 

146def main(): 

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

148 parser = argparse.ArgumentParser( 

149 description="Merges several PDB files into one.", 

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

151 ) 

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

153 

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

155 required_args.add_argument( 

156 "--input_file_path", 

157 required=True, 

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

159 ) 

160 required_args.add_argument( 

161 "--output_file_path", 

162 required=True, 

163 help="Description for the output file path. Accepted formats: zip.", 

164 ) 

165 

166 args = parser.parse_args() 

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

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

169 biobb_pdb_merge( 

170 input_file_path=args.input_file_path, 

171 output_file_path=args.output_file_path, 

172 properties=properties, 

173 ) 

174 

175 

176if __name__ == "__main__": 

177 main()