Source code for stiffness.basepair_stiffness

#!/usr/bin/env python3

"""Module containing the HelParStiffness class and the command line interface."""
import argparse
from pathlib import Path

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt

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_dna.utils.loader import load_data


[docs]class BPStiffness(BiobbObject): """ | biobb_dna BPStiffness | Calculate stiffness constants matrix between all six helical parameters for a single base pair step. Args: input_filename_shift (str): Path to csv file with data for helical parameter 'shift'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_shift_AA.csv>`_. Accepted formats: csv (edam:format_3752) input_filename_slide (str): Path to csv file with data for helical parameter 'slide'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_slide_AA.csv>`_. Accepted formats: csv (edam:format_3752) input_filename_rise (str): Path to csv file with data for helical parameter 'rise'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_rise_AA.csv>`_. Accepted formats: csv (edam:format_3752) input_filename_tilt (str): Path to csv file with data for helical parameter 'tilt'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_tilt_AA.csv>`_. Accepted formats: csv (edam:format_3752) input_filename_roll (str): Path to csv file with data for helical parameter 'roll'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_roll_AA.csv>`_. Accepted formats: csv (edam:format_3752) input_filename_twist (str): Path to csv file with data for helical parameter 'twist'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_twist_AA.csv>`_. Accepted formats: csv (edam:format_3752) output_csv_path (str): Path to directory where stiffness matrix file is saved as a csv file. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffbp_ref.csv>`_. Accepted formats: csv (edam:format_3752) output_jpg_path (str): Path to directory where stiffness heatmap image is saved as a jpg file. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg>`_. Accepted formats: jpg (edam:format_3579) properties (dict): * **KT** (*float*) - (0.592186827) Value of Boltzmann temperature factor. * **scaling** (*list*) - ([1, 1, 1, 10.6, 10.6, 10.6]) Values by which to scale stiffness. Positions correspond to helical parameters in the order: shift, slide, rise, tilt, roll, twist. * **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_dna.stiffness.basepair_stiffness import basepair_stiffness prop = { 'KT': 0.592186827, 'scaling': [1, 1, 1, 10.6, 10.6, 10.6] } basepair_stiffness( input_filename_shift='path/to/basepair/shift.csv', input_filename_slide='path/to/basepair/slide.csv', input_filename_rise='path/to/basepair/rise.csv', input_filename_tilt='path/to/basepair/tilt.csv', input_filename_roll='path/to/basepair/roll.csv', input_filename_twist='path/to/basepair/twist.csv', output_csv_path='path/to/output/file.csv', output_jpg_path='path/to/output/plot.jpg', 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_filename_shift, input_filename_slide, input_filename_rise, input_filename_tilt, input_filename_roll, input_filename_twist, output_csv_path, output_jpg_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 = { 'in': { 'input_filename_shift': input_filename_shift, 'input_filename_slide': input_filename_slide, 'input_filename_rise': input_filename_rise, 'input_filename_tilt': input_filename_tilt, 'input_filename_roll': input_filename_roll, 'input_filename_twist': input_filename_twist }, 'out': { 'output_csv_path': output_csv_path, 'output_jpg_path': output_jpg_path } } self.properties = properties self.KT = properties.get( "KT", 0.592186827) self.scaling = properties.get( "scaling", [1, 1, 1, 10.6, 10.6, 10.6]) # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`BPStiffness <stiffness.basepair_stiffness.BPStiffness>` object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Creating temporary folder self.tmp_folder = fu.create_unique_dir(prefix="bp_stiffness_") fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) # read input shift = load_data( self.io_dict["in"]["input_filename_shift"]) slide = load_data( self.io_dict["in"]["input_filename_slide"]) rise = load_data( self.io_dict["in"]["input_filename_rise"]) tilt = load_data( self.io_dict["in"]["input_filename_tilt"]) roll = load_data( self.io_dict["in"]["input_filename_roll"]) twist = load_data( self.io_dict["in"]["input_filename_twist"]) # build matrix cols_arr from helpar input data files coordinates = ["shift", "slide", "rise", "tilt", "roll", "twist"] basepairname = shift.columns[0] helpar_matrix = pd.concat( [shift, slide, rise, tilt, roll, twist], axis=1) helpar_matrix.columns = coordinates # covariance cov_df = helpar_matrix.cov() # stiffness stiff = np.linalg.inv(cov_df) * self.KT stiff_diag = stiff * np.array(self.scaling) stiff_df = pd.DataFrame( stiff_diag, columns=cov_df.columns, index=cov_df.index) stiff_df.index.name = basepairname # save csv data stiff_df.to_csv(Path(self.io_dict["out"]["output_csv_path"])) # create heatmap fig, axs = plt.subplots(1, 1, dpi=300, tight_layout=True) axs.pcolor(stiff_df) # Loop over data dimensions and create text annotations. for i in range(len(stiff_df)): for j in range(len(stiff_df)): axs.text( j+.5, i+.5, f"{stiff_df[coordinates[j]].loc[coordinates[i]]:.2f}", ha="center", va="center", color="w") axs.text( 0, -1.35, "Units:\n" "Diagonal Shift/Slide/Rise in kcal/(mol*Ų), Diagonal Tilt/Roll/Twist in kcal/(mol*degree²)\n" "Out of Diagonal: Shift/Slide/Rise in kcal/(mol*Å), Out of Diagonal Tilt/Roll/Twist in kcal/(mol*degree)", fontsize=6) axs.set_xticks([i + 0.5 for i in range(len(stiff_df))]) axs.set_xticklabels(stiff_df.columns, rotation=90) axs.set_yticks([i+0.5 for i in range(len(stiff_df))]) axs.set_yticklabels(stiff_df.index) axs.set_title( f"Stiffness Constants for Base Pair Step \'{basepairname}\'") fig.tight_layout() fig.savefig( self.io_dict['out']['output_jpg_path'], format="jpg") plt.close() # Remove temporary file(s) 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 basepair_stiffness( input_filename_shift: str, input_filename_slide: str, input_filename_rise: str, input_filename_tilt: str, input_filename_roll: str, input_filename_twist: str, output_csv_path: str, output_jpg_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`BPStiffness <stiffness.basepair_stiffness.BPStiffness>` class and execute the :meth:`launch() <stiffness.basepair_stiffness.BPStiffness.BPStiffness.launch>` method.""" return BPStiffness( input_filename_shift=input_filename_shift, input_filename_slide=input_filename_slide, input_filename_rise=input_filename_rise, input_filename_tilt=input_filename_tilt, input_filename_roll=input_filename_roll, input_filename_twist=input_filename_twist, output_csv_path=output_csv_path, output_jpg_path=output_jpg_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='Calculate stiffness constants matrix between all six helical parameters for a single base pair step.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_filename_shift', required=True, help='Path to csv file with shift inputs. Accepted formats: csv.') required_args.add_argument('--input_filename_slide', required=True, help='Path to csv file with slide inputs. Accepted formats: csv.') required_args.add_argument('--input_filename_rise', required=True, help='Path to csv file with rise inputs. Accepted formats: csv.') required_args.add_argument('--input_filename_tilt', required=True, help='Path to csv file with tilt inputs. Accepted formats: csv.') required_args.add_argument('--input_filename_roll', required=True, help='Path to csv file with roll inputs. Accepted formats: csv.') required_args.add_argument('--input_filename_twist', required=True, help='Path to csv file with twist inputs. Accepted formats: csv.') required_args.add_argument('--output_csv_path', required=True, help='Path to output covariance data file. Accepted formats: csv.') required_args.add_argument('--output_jpg_path', required=True, help='Path to output covariance data file. Accepted formats: csv.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() basepair_stiffness( input_filename_shift=args.input_filename_shift, input_filename_slide=args.input_filename_slide, input_filename_rise=args.input_filename_rise, input_filename_tilt=args.input_filename_tilt, input_filename_roll=args.input_filename_roll, input_filename_twist=args.input_filename_twist, output_csv_path=args.output_csv_path, output_jpg_path=args.output_jpg_path, properties=properties)
if __name__ == '__main__': main()