Source code for fpocket.fpocket_filter

#!/usr/bin/env python3

"""Module containing the FPocketFilter class and the command line interface."""

import argparse
import json
from typing import Optional

from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
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,
)
from biobb_vs.utils.common import _from_string_to_list


[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. * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. 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 = [ float(elem) for elem in _from_string_to_list(properties.get("score", None)) ] self.druggability_score = [ float(elem) for elem in _from_string_to_list(properties.get("druggability_score", None)) ] self.volume = [ float(elem) for elem in _from_string_to_list(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: Optional[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() fpocket_filter.__doc__ = FPocketFilter.__doc__
[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()