Source code for pygenprop.tree

#!/usr/bin/env python

Created by: Lee Bergstrand (2018)

Description: The genome property tree class.

import json
import csv

[docs]class GenomePropertiesTree(object): """ This class contains a representation of a set of nested genome properties. Internally, the instantiated object contains a rooted DAG of genome properties connected from root to leaf (parent to child). A dictionary is also included which points to each tree node for fast lookups by genome property identifier. """ def __init__(self, *genome_properties): """ When the object is created create a dictionary and connect the nodes to each other to form the polytree. :param genome_properties: One or more genome property objects. """ self.genome_properties_dictionary = {} for new_property in genome_properties: new_property.tree = self self.genome_properties_dictionary[] = new_property self.build_genome_property_connections() @property def root(self): """ Gets the top level genome properties object in a genome properties tree. :return: The root genome property of the genome properties tree. """ genome_property = next(iter(self.genome_properties_dictionary.values())) while True: if genome_property.parents: genome_property = genome_property.parents[0] else: break return genome_property @property def leafs(self): """ Returns the leaf nodes of the rooted DAG. :return: A list of all genome property objects with no children. """ for genome_property in self: if not genome_property.children: yield genome_property
[docs] def build_genome_property_connections(self): """ Build connections between parent-child genome properties in the dictionary. This creates the rooted DAG. """ for genome_property in self: child_identifiers = genome_property.child_genome_property_identifiers for identifier in child_identifiers: child_genome_property = self[identifier] if child_genome_property: genome_property.children.append(child_genome_property) child_genome_property.parents.append(genome_property)
[docs] def to_json(self, nodes_and_links=False): """ Converts the object to a JSON representation. :param nodes_and_links: If True, returns the JSON in node and link format. :return: A JSON formatted string representing the genome property tree. """ if nodes_and_links: nodes = self.create_graph_nodes_json(as_list=True) links = self.create_graph_links_json(as_list=True) final_json = json.dumps({'nodes': nodes, 'links': links}) else: final_json = self.create_nested_json() return final_json
[docs] def create_nested_json(self, current_property=None, as_dict=False): """ Converts the object to a nested JSON representation. :param current_property: The current root genome property (for recursion) :param as_dict: Returns Return a dictionary for incorporation into other json objects. :return: A JSON formatted string or dictionary representing the object. """ if current_property: root_genome_property = current_property else: root_genome_property = self.root root_json = root_genome_property.to_json(as_dict=True) child_jsons = [] for child in root_genome_property.children: child_json = self.create_nested_json(child, as_dict=True) child_jsons.append(child_json) root_json['children'] = child_jsons if as_dict: output = root_json else: output = json.dumps(root_json) return output
[docs] def create_graph_nodes_json(self, as_list=False): """ Creates a JSON representation of a genome property dictionary. :param as_list: Return as a list instead of a JSON formatted string. :return: A JSON formatted string of a list of each properties JSON representation. """ nodes = [] for genome_property in self: genome_property_dict = genome_property.to_json(as_dict=True) nodes.append(genome_property_dict) if as_list: output = nodes else: output = json.dumps(nodes) return output
@property def genome_property_identifiers(self): """ The identifiers all genome properties in the database. :return: A set of all genome property identifiers. """ return set( for genome_property in self) @property def consortium_identifiers(self): """ All InterPro consortium signature identifiers (PFAM, TIGRFAM, etc.) used by the genome properties database. :return: A set of all unique consortium identifiers used in genome properties. """ return self.get_evidence_identifiers(consortium=True) @property def interpro_identifiers(self): """ All global InterPro identifiers (IPRXXXX, etc.) used by the genome properties database. :return: A set of all unique InterPro identifiers used in genome properties. """ return self.get_evidence_identifiers()
[docs] def get_evidence_identifiers(self, consortium=False): """ Gets evidence identifiers from all genome properties in the database. :param consortium: If true, list the consortium signature identifiers (PFAM, TIGRFAM) :return: A set of all unique evidence identifiers used in genome properties. """ global_identifiers = [] for genome_property in self: for step in genome_property.steps: for functional_element in step.functional_elements: for evidence in functional_element.evidence: if consortium: current_identifiers = evidence.consortium_identifiers else: current_identifiers = evidence.interpro_identifiers if current_identifiers: global_identifiers.extend(current_identifiers) return set(global_identifiers)
[docs] def create_metabolism_database_mapping_file(self, file_handle): """ Writes a mapping file which maps each genome property to KEGG and MetaCyc. :param file_handle: A python file handle object. """ mapping_data = [] for genome_property in self: for database in genome_property.databases: if database.database_name in ['MetaCyc', 'KEGG']: row = (,, database.database_name, database.record_title, database.record_ids[0]) sanitized_row = [data_point.replace(',', '') for data_point in row] mapping_data.append(sanitized_row) csv.writer(file_handle).writerows(mapping_data)
def __getitem__(self, item): return self.genome_properties_dictionary.get(item) def __len__(self): return len(self.genome_properties_dictionary) def __iter__(self): for genome_property in self.genome_properties_dictionary.values(): yield genome_property def __contains__(self, item): return True if item in self.genome_properties_dictionary else False def __repr__(self): repr_data = [] for genome_property in self: repr_data.append(str(genome_property)) return '\n'.join(repr_data) def __str__(self): """ Prints a human readable summary for all properties in a genome properties dictionary. """ for genome_property in self: parent_ids = [ for parent in genome_property.parents] child_ids = [ for child in genome_property.children] if not parent_ids: parent_ids = "[ No Parent Genome Properties ]" if not child_ids: child_ids = "[ No Child Properties ]" print( "\n" + + " (" + + ")" + " Type: [" + genome_property.type + "]" + " Parents: " + str(parent_ids) + " Children: " + str(child_ids)) print( '=====================================================================================================') for step in genome_property.steps: print(str(step) + "\n")