Source code for utils.pairwise_comparison

#!/usr/bin/env python3

"""Module containing the PairwiseComparison class and the command line interface."""
import argparse
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
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_ml.utils.common import check_input_path, check_output_path, getHeader, getIndependentVarsList, getIndependentVars


[docs]class PairwiseComparison(BiobbObject): """ | biobb_ml PairwiseComparison | Generates a pairwise comparison from a given dataset. Args: input_dataset_path (str): Path to the input dataset. File type: input. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/data/utils/dataset_pairwise_comparison.csv>`_. Accepted formats: csv (edam:format_3752). output_plot_path (str): Path to the pairwise comparison plot. File type: output. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/utils/ref_output_plot_pairwise_comparison.png>`_. Accepted formats: png (edam:format_3603). properties (dic): * **features** (*dict*) - ({}) Independent variables or columns from your dataset you want to compare. You can specify either a list of columns names from your input dataset, a list of columns indexes or a range of columns indexes. Formats: { "columns": ["column1", "column2"] } or { "indexes": [0, 2, 3, 10, 11, 17] } or { "range": [[0, 20], [50, 102]] }. In case of mulitple formats, the first one will be picked. * **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_ml.utils.pairwise_comparison import pairwise_comparison prop = { 'features': { 'columns': [ 'column1', 'column2', 'column3' ] } } pairwise_comparison(input_dataset_path='/path/to/myDataset.csv', output_plot_path='/path/to/newPlot.png', 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_dataset_path, output_plot_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_dataset_path": input_dataset_path}, "out": {"output_plot_path": output_plot_path} } # Properties specific for BB self.features = properties.get('features', {}) 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_dataset_path"] = check_input_path(self.io_dict["in"]["input_dataset_path"], "input_dataset_path", out_log, self.__class__.__name__) self.io_dict["out"]["output_plot_path"] = check_output_path(self.io_dict["out"]["output_plot_path"], "output_plot_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`PairwiseComparison <utils.pairwise_comparison.PairwiseComparison>` utils.pairwise_comparison.PairwiseComparison 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 dataset fu.log('Getting dataset from %s' % self.io_dict["in"]["input_dataset_path"], self.out_log, self.global_log) if 'columns' in self.features: labels = getHeader(self.io_dict["in"]["input_dataset_path"]) skiprows = 1 else: labels = None skiprows = None data = pd.read_csv(self.io_dict["in"]["input_dataset_path"], header=None, sep="\\s+|;|:|,|\t", engine="python", skiprows=skiprows, names=labels) fu.log('Parsing [%s] columns of the dataset' % getIndependentVarsList(self.features), self.out_log, self.global_log) if not self.features: cols = data[data.columns] else: cols = getIndependentVars(self.features, data, self.out_log, self.__class__.__name__) pp = sns.pairplot(cols, height=1.8, aspect=1.8, plot_kws=dict(edgecolor="k", linewidth=0.5), diag_kind="kde", diag_kws=dict(shade=True)) fig = pp.fig fig.subplots_adjust(top=0.93, wspace=0.3) fig.suptitle('Attributes Pairwise Plots', fontsize=14) plt.tight_layout(rect=[0, 0.03, 1, 0.95]) plt.savefig(self.io_dict["out"]["output_plot_path"], dpi=150) fu.log('Saving Pairwise Plot to %s' % self.io_dict["out"]["output_plot_path"], self.out_log, self.global_log) # Copy files to host self.copy_to_host() self.tmp_files.extend([ self.stage_io_dict.get("unique_dir") ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return 0
[docs]def pairwise_comparison(input_dataset_path: str, output_plot_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`PairwiseComparison <utils.pairwise_comparison.PairwiseComparison>` class and execute the :meth:`launch() <utils.pairwise_comparison.PairwiseComparison.launch>` method.""" return PairwiseComparison(input_dataset_path=input_dataset_path, output_plot_path=output_plot_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="Generates a pairwise comparison from a given dataset", 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_dataset_path', required=True, help='Path to the input dataset. Accepted formats: csv.') required_args.add_argument('--output_plot_path', required=True, help='Path to the pairwise comparison plot. Accepted formats: png.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block pairwise_comparison(input_dataset_path=args.input_dataset_path, output_plot_path=args.output_plot_path, properties=properties)
if __name__ == '__main__': main()