#!/usr/bin/env python
"""Module containing the CanonicalFasta class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
from biobb_io.api.common import check_output_path, check_mandatory_property, download_fasta, write_fasta
[docs]class CanonicalFasta(BiobbObject):
"""
| biobb_io CanonicalFasta
| This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.
| 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.
Args:
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).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **pdb_code** (*str*) - (None) RSCB PDB code.
* **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/>`_).
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_io.api.canonical_fasta import canonical_fasta
prop = {
'pdb_code': '4i23',
'api_id': 'pdb'
}
canonical_fasta(output_fasta_path='/path/to/newFasta.fasta',
properties=prop)
Info:
* wrapped_software:
* name: Protein Data Bank
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, output_fasta_path,
properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"out": {"output_fasta_path": output_fasta_path}
}
# Properties specific for BB
self.pdb_code = properties.get('pdb_code', None)
self.api_id = properties.get('api_id', 'pdbe')
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.output_fasta_path = check_output_path(self.io_dict["out"]["output_fasta_path"], "output_fasta_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`CanonicalFasta <api.canonical_fasta.CanonicalFasta>` api.canonical_fasta.CanonicalFasta object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
self.pdb_code = self.pdb_code.strip().lower()
# Downloading PDB file
pdb_string = download_fasta(self.pdb_code, self.api_id, self.out_log, self.global_log)
write_fasta(pdb_string, self.output_fasta_path, self.out_log, self.global_log)
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def canonical_fasta(output_fasta_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`CanonicalFasta <api.canonical_fasta.CanonicalFasta>` class and
execute the :meth:`launch() <api.canonical_fasta.CanonicalFasta.launch>` method."""
return CanonicalFasta(output_fasta_path=output_fasta_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
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))
parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('-o', '--output_fasta_path', required=True, help="Path to the canonical FASTA file. Accepted formats: fasta.")
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
canonical_fasta(output_fasta_path=args.output_fasta_path,
properties=properties)
if __name__ == '__main__':
main()