#!/usr/bin/env python3
"""Module containing the FPocketFilter class and the command line interface."""
import argparse
import json
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_vs.fpocket.common import check_input_path, check_output_path, check_range, process_output_fpocket_filter
[docs]class FPocketFilter(BiobbObject):
"""
| biobb_vs FPocketFilter
| Performs a search over the outputs of the fpocket building block.
| Finds one or more binding sites in the outputs of the fpocket building block from given parameters.
Args:
input_pockets_zip (str): Path to all the pockets found by fpocket. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_pockets.zip>`_. Accepted formats: zip (edam:format_3987).
input_summary (str): Path to the JSON summary file returned by fpocket. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_summary.json>`_. Accepted formats: json (edam:format_3464).
output_filter_pockets_zip (str): Path to the selected pockets after filtering. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_filter_pockets.zip>`_. Accepted formats: zip (edam:format_3987).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **score** (*list*) - (None) List of two float numbers between 0 and 1 indicating the score range. Indicates the fpocket score after the evaluation of pocket prediction accuracy as defined in the `fpocket paper <https://doi.org/10.1186/1471-2105-10-168>`_.
* **druggability_score** (*list*) - (None) List of two float numbers between 0 and 1 indicating the druggability_score range. It's a value between 0 and 1, 0 signifying that the pocket is likely to not bind a drug like molecule and 1, that it is very likely to bind the latter.
* **volume** (*list*) - (None) List of two float numbers indicating the volume range. Indicates the pocket volume.
* **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_vs.fpocket.fpocket_filter import fpocket_filter
prop = {
'score': [0.2, 1],
'druggability_score': [0.2, 0.8],
'volume': [100, 600.2]
}
fpocket_filter(input_pockets_zip='/path/to/myPockets.zip',
input_summary='/path/to/mySummary.json',
output_filter_pockets_zip='/path/to/newPockets.json',
properties=prop)
Info:
* wrapped_software:
* name: In house
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pockets_zip, input_summary, output_filter_pockets_zip,
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 = {
"in": {"input_pockets_zip": input_pockets_zip, "input_summary": input_summary},
"out": {"output_filter_pockets_zip": output_filter_pockets_zip}
}
# Properties specific for BB
self.score = properties.get('score', None)
self.druggability_score = properties.get('druggability_score', None)
self.volume = properties.get('volume', None)
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.io_dict["in"]["input_pockets_zip"] = check_input_path(self.io_dict["in"]["input_pockets_zip"], "input_pockets_zip", out_log, self.__class__.__name__)
self.io_dict["in"]["input_summary"] = check_output_path(self.io_dict["in"]["input_summary"], "input_summary", False, out_log, self.__class__.__name__)
self.io_dict["out"]["output_filter_pockets_zip"] = check_output_path(self.io_dict["out"]["output_filter_pockets_zip"], "output_filter_pockets_zip", True, out_log, self.__class__.__name__)
[docs] def score_matcher(self, score):
return lambda d: d['score'] > score[0] and d['score'] <= score[1]
[docs] def druggability_score_matcher(self, druggability_score):
return lambda d: d['druggability_score'] > druggability_score[0] and d['druggability_score'] <= druggability_score[1]
[docs] def volume_matcher(self, volume):
return lambda d: d['volume'] > volume[0] and d['volume'] <= volume[1]
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`FPocketFilter <fpocket.fpocket_filter.FPocketFilter>` fpocket.fpocket_filter.FPocketFilter 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
self.stage_files()
# load input_summary into a dictionary
with open(self.io_dict["in"]["input_summary"]) as json_file:
data = json.load(json_file)
# build search_list
search_list = []
ranges = {}
if self.score:
check_range('score', self.score, [0, 1], self.out_log, self.__class__.__name__)
search_list.append(self.score_matcher(self.score))
ranges['score'] = self.score
if self.druggability_score:
check_range('druggability_score', self.druggability_score, [0, 1], self.out_log, self.__class__.__name__)
search_list.append(self.druggability_score_matcher(self.druggability_score))
ranges['druggability_score'] = self.druggability_score
if self.volume:
check_range('volume', self.volume, [0, 10000], self.out_log, self.__class__.__name__)
search_list.append(self.volume_matcher(self.volume))
ranges['volume'] = self.volume
fu.log('Performing a search under the next parameters: %s' % (', '.join(['{0}: {1}'.format(k, v) for k, v in ranges.items()])), self.out_log)
# perform search
search = [x for x in data if all([f(data[x]) for f in search_list])]
if len(search) == 0:
fu.log('No matches found', self.out_log)
return 0
str_out = ''
for s in search:
str_out = str_out + ('\n**********\n%s\n**********\nscore: %s\ndruggability_score: %s\nvolume: %s\n' % (s, data[s]["score"], data[s]["druggability_score"], data[s]["volume"]))
fu.log('Found %d matches:%s' % (len(search), str_out), self.out_log)
# create tmp_folder
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
process_output_fpocket_filter(search,
self.tmp_folder,
self.io_dict["in"]["input_pockets_zip"],
self.io_dict["out"]["output_filter_pockets_zip"],
self.remove_tmp,
self.out_log)
# Copy files to host
self.copy_to_host()
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
self.tmp_folder
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def fpocket_filter(input_pockets_zip: str, input_summary: str, output_filter_pockets_zip: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`FPocketFilter <fpocket.fpocket_filter.FPocketFilter>` class and
execute the :meth:`launch() <fpocket.fpocket_filter.FPocketFilter.launch>` method."""
return FPocketFilter(input_pockets_zip=input_pockets_zip,
input_summary=input_summary,
output_filter_pockets_zip=output_filter_pockets_zip,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Finds one or more binding sites in the outputs of the fpocket building block from given parameters.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_pockets_zip', required=True, help='Path to all the pockets found by fpocket. Accepted formats: zip.')
required_args.add_argument('--input_summary', required=True, help='Path to the JSON summary file returned by fpocket. Accepted formats: json.')
required_args.add_argument('--output_filter_pockets_zip', required=True, help='Path to the selected pockets after filtering. Accepted formats: zip.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
fpocket_filter(input_pockets_zip=args.input_pockets_zip,
input_summary=args.input_summary,
output_filter_pockets_zip=args.output_filter_pockets_zip,
properties=properties)
if __name__ == '__main__':
main()