Source code for pygenprop.genome_property

#!/usr/bin/env python

Created by: Lee Bergstrand (2017)

Description: The genome property class.

import json

[docs]class GenomeProperty(object): """ Represents a EBI genome property. Each represents specific capabilities of an organism as proven by the presence of genes found in its genome. """ def __init__(self, accession_id, name, property_type, threshold=0, parents=None, children=None, references=None, databases=None, steps=None, public=True, description=None, private_notes=None, tree=None): """ Creates a new GenomeProperty object. :param accession_id: The genome property accession (i.e. "GenProp00286"). :param name: The name of the genome property. :param property_type: The type of genome property (ex. "METAPATH"). :param threshold: Is a threshold that the number of required steps must exceed. :param parents: The parent genome property of the current genome property (parent accession or direct link). :param references: A list of reference objects which help support the existence of the property. :param databases: A list of database objects which represent database entries related to the property. :param steps: A list of step objects that are part of the property. :param public: Boolean detailing if the genome property should be public. :param description: A detailed description of the genome property. :param private_notes: Private notes about the property a potential problems with it. :param tree: The tree for which the genome property belongs too. """ if children is None: children = [] if parents is None: parents = [] if steps is None: steps = [] if databases is None: databases = [] if references is None: references = [] if threshold is None: threshold = 0 = accession_id = name self.type = property_type self.threshold = int(threshold) self.references = references self.databases = databases self.parents = parents self.children = children self.steps = steps self.public = public self.description = description self.private_notes = private_notes self.tree = tree def __repr__(self): has_references = False has_steps = False has_databases = False has_parents = False has_children = False if self.references: has_references = True if self.steps: has_steps = True if self.databases: has_databases = True if self.parents: has_parents = True if self.children: has_children = True repr_data = [str(, 'Type: ' + str(self.type), 'Name: ' + str(, 'Thresh: ' + str(self.threshold), 'References: ' + str(has_references), 'Databases: ' + str(has_databases), 'Steps: ' + str(has_steps), 'Parents: ' + str(has_parents), 'Children: ' + str(has_children), 'Public: ' + str(self.public)] return ', '.join(repr_data) @property def required_steps(self): """ Returns a list of all the required steps of the genome property. :return: All required steps as list. """ return [step for step in self.steps if step.required] @property def child_genome_property_identifiers(self): """ Collects the genome property identifiers of child genome properties. :return: A list of genome property identifiers. """ child_genome_properties_identifiers = [] for step in self.steps: child_genome_properties_identifiers.extend(step.genome_property_identifiers) return child_genome_properties_identifiers
[docs] def to_json(self, as_dict=False): """ Converts the object to a JSON representation. :param as_dict: Return a dictionary for incorporation into other json objects. :return: A JSON formatted string or dictionary representing the object. """ json_dict = { 'id':, 'name':, 'type': self.type, 'description': self.description, 'notes': self.private_notes } if as_dict: output = json_dict else: output = json.dumps(json_dict) return output