Coverage for biobb_flexserv/pcasuite/pcz_unzip.py: 88%

1#!/usr/bin/env python3 

2 

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

4from typing import Optional 

5from pathlib import PurePath 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools.file_utils import launchlogger 

8 

9 

10class PCZunzip(BiobbObject): 

11 """ 

12 | biobb_flexserv PCZunzip 

13 | Wrapper of the pcaunzip tool from the PCAsuite FlexServ module. 

14 | Uncompress Molecular Dynamics (MD) trajectories compressed using Principal Component Analysis (PCA) algorithms. 

15 

16 Args: 

17 input_pcz_path (str): Input compressed trajectory. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz>`_. Accepted formats: pcz (edam:format_3874). 

18 output_crd_path (str): Output uncompressed trajectory. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/traj.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), pdb (edam:format_1476). 

19 properties (dict - Python dictionary object containing the tool parameters, not input/output files): 

20 * **binary_path** (*str*) - ("pcaunzip") pcaunzip binary path to be used. 

21 * **verbose** (*bool*) - (False) Make output verbose 

22 * **pdb** (*bool*) - (False) Use PDB format for output trajectory 

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

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

25 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. 

26 * **container_path** (*str*) - (None) Container path definition. 

27 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition. 

28 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. 

29 * **container_working_dir** (*str*) - (None) Container working directory definition. 

30 * **container_user_id** (*str*) - (None) Container user_id definition. 

31 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. 

32 

33 Examples: 

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

35 

36 from biobb_flexserv.pcasuite.pcz_unzip import pcz_unzip 

37 prop = { 

38 'pdb': False 

39 } 

40 pcz_unzip( input_pcz_path='/path/to/pcazip_input.pcz', 

41 output_crd_path='/path/to/pcazip_traj.crd', 

42 properties=prop) 

43 

44 Info: 

45 * wrapped_software: 

46 * name: FlexServ PCAsuite 

47 * version: >=1.0 

48 * license: Apache-2.0 

49 * ontology: 

50 * name: EDAM 

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

52 

53 """ 

54 

55 def __init__(self, input_pcz_path: str, 

56 output_crd_path: str, properties: Optional[dict] = None, **kwargs) -> None: 

57 

58 properties = properties or {} 

59 

60 # Call parent class constructor 

61 super().__init__(properties) 

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

63 

64 # Input/Output files 

65 self.io_dict = { 

66 'in': {'input_pcz_path': input_pcz_path}, 

67 'out': {'output_crd_path': output_crd_path} 

68 } 

69 

70 # Properties specific for BB 

71 self.properties = properties 

72 self.binary_path = properties.get('binary_path', 'pcaunzip') 

73 self.verbose = properties.get('verbose', False) 

74 self.pdb = properties.get('pdb', False) 

75 

76 # Check the properties 

77 self.check_properties(properties) 

78 self.check_arguments() 

79 

80 @launchlogger 

81 def launch(self): 

82 """Launches the execution of the FlexServ pcaunzip module.""" 

83 

84 # Setup Biobb 

85 if self.check_restart(): 

86 return 0 

87 self.stage_files() 

88 

89 if self.container_path: 

90 working_dir = self.container_volume_path if self.container_volume_path else "/data" 

91 else: 

92 working_dir = self.stage_io_dict.get("unique_dir", "") 

93 

94 # Command line 

95 # pcaunzip -i infile [-o outfile] [--pdb] [--verbose] [--help] 

96 # self.cmd = [self.binary_path, 

97 # "-i", input_pcz, 

98 # "-o", output_crd 

99 # ] 

100 

101 self.cmd = ['cd', working_dir, ';', 

102 self.binary_path, 

103 "-i", PurePath(self.stage_io_dict["in"]["input_pcz_path"]).name, 

104 "-o", PurePath(self.stage_io_dict["out"]["output_crd_path"]).name 

105 ] 

106 

107 if self.verbose: 

108 self.cmd.append('-v') 

109 

110 if self.pdb: 

111 self.cmd.append('--pdb') 

112 

113 # Run Biobb block 

114 self.run_biobb() 

115 

116 # Copy files to host 

117 self.copy_to_host() 

118 

119 # Remove temporary folder(s) 

120 self.remove_tmp_files() 

121 

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

123 

124 return self.return_code 

125 

126 

127def pcz_unzip(input_pcz_path: str, 

128 output_crd_path: str, 

129 properties: Optional[dict] = None, **kwargs) -> int: 

130 """Create :class:`PCZunzip <flexserv.pcasuite.PCZunzip>`flexserv.pcasuite.PCZunzip class and 

131 execute :meth:`launch() <flexserv.pcasuite.PCZunzip.launch>` method""" 

132 return PCZunzip(**dict(locals())).launch() 

133 

134 

135pcz_unzip.__doc__ = PCZunzip.__doc__ 

136main = PCZunzip.get_main(pcz_unzip, "Uncompress Molecular Dynamics (MD) compressed trajectories using Principal Component Analysis (PCA) algorithms.") 

137 

138if __name__ == '__main__': 

139 main()