Coverage for biobb_io/api/canonical_fasta.py: 76%
42 statements
« prev ^ index » next coverage.py v7.5.3, created at 2024-06-14 18:20 +0000
« prev ^ index » next coverage.py v7.5.3, created at 2024-06-14 18:20 +0000
1#!/usr/bin/env python
3"""Module containing the CanonicalFasta class and the command line interface."""
4import argparse
5from biobb_common.generic.biobb_object import BiobbObject
6from biobb_common.configuration import settings
7from biobb_common.tools.file_utils import launchlogger
8from biobb_io.api.common import check_output_path, check_mandatory_property, download_fasta, write_fasta
11class CanonicalFasta(BiobbObject):
12 """
13 | biobb_io CanonicalFasta
14 | This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.
15 | Wrapper for the `Protein Data Bank <https://www.rcsb.org/>`_ and the `MMB PDB mirror <http://mmb.irbbarcelona.org/api/>`_ for downloading a single FASTA structure.
17 Args:
18 output_fasta_path (str): Path to the canonical FASTA file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/canonical_fasta.fasta>`_. Accepted formats: fasta (edam:format_1929).
19 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
20 * **pdb_code** (*str*) - (None) RSCB PDB code.
21 * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), mmb (`MMB PDB mirror API <http://mmb.irbbarcelona.org/api/>`_).
22 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
23 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
24 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
26 Examples:
27 This is a use example of how to use the building block from Python::
29 from biobb_io.api.canonical_fasta import canonical_fasta
30 prop = {
31 'pdb_code': '4i23',
32 'api_id': 'pdb'
33 }
34 canonical_fasta(output_fasta_path='/path/to/newFasta.fasta',
35 properties=prop)
37 Info:
38 * wrapped_software:
39 * name: Protein Data Bank
40 * license: Apache-2.0
41 * ontology:
42 * name: EDAM
43 * schema: http://edamontology.org/EDAM.owl
45 """
47 def __init__(self, output_fasta_path,
48 properties=None, **kwargs) -> None:
49 properties = properties or {}
51 # Call parent class constructor
52 super().__init__(properties)
53 self.locals_var_dict = locals().copy()
55 # Input/Output files
56 self.io_dict = {
57 "out": {"output_fasta_path": output_fasta_path}
58 }
60 # Properties specific for BB
61 self.pdb_code = properties.get('pdb_code', None)
62 self.api_id = properties.get('api_id', 'pdbe')
63 self.properties = properties
65 # Check the properties
66 self.check_properties(properties)
67 self.check_arguments()
69 def check_data_params(self, out_log, err_log):
70 """ Checks all the input/output paths and parameters """
71 self.output_fasta_path = check_output_path(self.io_dict["out"]["output_fasta_path"], "output_fasta_path", False, out_log, self.__class__.__name__)
73 @launchlogger
74 def launch(self) -> int:
75 """Execute the :class:`CanonicalFasta <api.canonical_fasta.CanonicalFasta>` api.canonical_fasta.CanonicalFasta object."""
77 # check input/output paths and parameters
78 self.check_data_params(self.out_log, self.err_log)
80 # Setup Biobb
81 if self.check_restart():
82 return 0
84 check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
86 self.pdb_code = self.pdb_code.strip().lower()
88 # Downloading PDB file
89 pdb_string = download_fasta(self.pdb_code, self.api_id, self.out_log, self.global_log)
90 write_fasta(pdb_string, self.output_fasta_path, self.out_log, self.global_log)
92 self.check_arguments(output_files_created=True, raise_exception=False)
94 return 0
97def canonical_fasta(output_fasta_path: str, properties: dict = None, **kwargs) -> int:
98 """Execute the :class:`CanonicalFasta <api.canonical_fasta.CanonicalFasta>` class and
99 execute the :meth:`launch() <api.canonical_fasta.CanonicalFasta.launch>` method."""
101 return CanonicalFasta(output_fasta_path=output_fasta_path,
102 properties=properties, **kwargs).launch()
105def main():
106 """Command line execution of this building block. Please check the command line documentation."""
107 parser = argparse.ArgumentParser(description="This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
108 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
110 # Specific args of each building block
111 required_args = parser.add_argument_group('required arguments')
112 required_args.add_argument('-o', '--output_fasta_path', required=True, help="Path to the canonical FASTA file. Accepted formats: fasta.")
114 args = parser.parse_args()
115 config = args.config if args.config else None
116 properties = settings.ConfReader(config=config).get_prop_dic()
118 # Specific call of each building block
119 canonical_fasta(output_fasta_path=args.output_fasta_path,
120 properties=properties)
123if __name__ == '__main__':
124 main()