Source code for pygenprop.step

#!/usr/bin/env python

Created by: Lee Bergstrand (2017)

Description: The step class.

from pygenprop.genome_property import GenomeProperty

[docs]class Step(object): """A class representing a step that supports the existence of a genome property.""" def __init__(self, number, functional_elements: list=None, parent: GenomeProperty=None): """ Creates a new Step object. :param number: The position of the step in the step list. :param functional_elements: A list of FunctionalElements supporting this step. """ if functional_elements is None: functional_elements = [] else: # Double link functional_elements back to the parent step. for element in functional_elements: element.parent = self self.number = int(number) self.functional_elements = functional_elements self.parent = parent def __repr__(self): repr_data = ['Step ' + str(self.number), 'Functional_Elements: ' + str(self.functional_elements)] return ', '.join(repr_data) @property def name(self): """ Get the name for a step based on combine the names of its functional elements. :return: The name of the step. """ return " ".join( for element in self.functional_elements) @property def required(self): """ Checks if the step is required by checking if any of the functional elements are required. :return: True if the step is required. """ required_step = False for element in self.functional_elements: if element.required: required_step = True break return required_step @property def genome_property_identifiers(self): """ Collects all the genome properties identifiers supporting a step. :return: A list of the steps child genome property identifiers. """ genome_properties_identifiers = [] for element in self.functional_elements: for evidence in element.evidence: if evidence.has_genome_property: genome_properties_identifiers.extend(evidence.genome_property_identifiers) return genome_properties_identifiers @property def genome_properties(self): """ Collects all the child genome properties supporting a step. :return: A list of child genome properties for a step. """ child_identifiers = self.genome_property_identifiers return [child_property for child_property in self.parent.children if in child_identifiers]