py3plex.algorithms.hedwig.core package¶

Submodules¶

py3plex.algorithms.hedwig.core.converters module¶

py3plex.algorithms.hedwig.core.converters.convert_mapping_to_rdf(input_mapping_file, extract_subnode_info=False, split_node_by=':', keep_index=1, layer_type='uniprotkb', annotation_mapping_file='test.gaf', go_identifier='GO:', prepend_string=None)¶

py3plex.algorithms.hedwig.core.converters.obo2n3(obofile, n3out, gaf_file)¶

py3plex.algorithms.hedwig.core.example module¶

Example-related classes.

@author: anze.vavpetic@ijs.si

class py3plex.algorithms.hedwig.core.example.Example(id, label, score, annotations=[], weights={})¶

Bases: object

Represents an example with its score, label, id and annotations.

ClassLabeled = 'class'¶

Ranked = 'ranked'¶

py3plex.algorithms.hedwig.core.helpers module¶

Helper functions.

@author: anze.vavpetic@ijs.si

py3plex.algorithms.hedwig.core.helpers.anonymous_uri(uri)¶

py3plex.algorithms.hedwig.core.helpers.avg(x)¶

py3plex.algorithms.hedwig.core.helpers.std(x)¶

py3plex.algorithms.hedwig.core.helpers.user_defined(uri)¶: Is this resource user defined?

py3plex.algorithms.hedwig.core.kb module¶

Knowledge-base class.

@author: anze.vavpetic@ijs.si

class py3plex.algorithms.hedwig.core.kb.ExperimentKB(triplets, score_fun, instances_as_leaves=True)¶

Bases: object

The knowledge base for one specific experiment.

add_sub_class(sub, obj)¶: Adds the resource ‘sub’ as a subclass of ‘obj’.

bits_to_indices(bits)¶: Converts the bitset to a set of indices.

get_domains(predicate)¶: Returns the bitsets for input and outputexamples of the binary predicate ‘predicate’.

get_empty_domain()¶: Returns a bitset covering no examples.

get_examples()¶: Returns all examples for this experiment.

get_full_domain()¶: Returns a bitset covering all examples.

get_members(predicate, bit=True)¶: Returns the examples for this predicate, either as a bitset or a set of ids.

get_reverse_members(predicate, bit=True)¶: Returns the examples for this predicate, either as a bitset or a set of ids.

get_root()¶: Root predicate, which covers all examples.

get_score(ex_idx)¶: Returns the score for example id ‘ex_idx’.

get_subclasses(predicate, producer_pred=None)¶: Returns a list of subclasses (as predicate objects) for ‘predicate’.

indices_to_bits(indices)¶: Converts the indices to a bitset.

is_discrete_target()¶

n_examples()¶: Returns the number of examples.

n_members(predicate)¶

super_classes(pred)¶: Returns all super classes of pred (with transitivity).

py3plex.algorithms.hedwig.core.load module¶

Reading input data.

@author: anze.vavpetic@ijs.si

py3plex.algorithms.hedwig.core.load.build_uri(class_string)¶: Checks if the string is a proper URI, if not it builds an URI with the generic namespace.

py3plex.algorithms.hedwig.core.load.csv(hierarchy_files, data)¶: Loads a simple hierarchy of features and data in csv format.

py3plex.algorithms.hedwig.core.load.csv_parse_data(g, data_file)¶

Assumes the following csv format:

example_uri_or_label; attr_uri_1; attr_uri_2; …; attr_uri_n http://example.org/uri_1; 0/1; 0/1; 0/1; 0/1; … http://example.org/uri_2; 0/1; 0/1; 0/1; 0/1; … …

Alternatively attribute values can be URIs themselves.

py3plex.algorithms.hedwig.core.load.csv_parse_hierarchy(g, path)¶

Assumes a hierarchy file of the following format:

class_1<tab>superclass_1_1; superclass_1_2; …; superclass_1_n class_2<tab>superclass_2_1; superclass_2_2; …; superclass_2_n … class_m<tab>superclass_m_1; superclass_m_2; …; superclass_m_n

py3plex.algorithms.hedwig.core.load.load_graph(ontology_list, data, def_format='n3', cache=True)¶

py3plex.algorithms.hedwig.core.load.rdf(paths, def_format='n3')¶: Loads the ontology into an rdf graph.

py3plex.algorithms.hedwig.core.predicate module¶

Predicate-related classes.

@author: anze.vavpetic@ijs.si

class py3plex.algorithms.hedwig.core.predicate.BinaryPredicate(label, pairs, kb, producer_pred=None)¶

Bases: py3plex.algorithms.hedwig.core.predicate.Predicate

A binary predicate.

class py3plex.algorithms.hedwig.core.predicate.Predicate(label, kb, producer_pred)¶

Bases: object

Represents a predicate as a member of a certain rule.

i = -1¶

class py3plex.algorithms.hedwig.core.predicate.UnaryPredicate(label, members, kb, producer_pred=None, custom_var_name=None, negated=False)¶

Bases: py3plex.algorithms.hedwig.core.predicate.Predicate

A unary predicate.

py3plex.algorithms.hedwig.core.rule module¶

The rule class.

@author: anze.vavpetic@ijs.si

class py3plex.algorithms.hedwig.core.rule.Rule(kb, predicates=[], target=None)¶

Bases: object

Represents a rule, along with its description, examples and statistics.

clone()¶: Returns a clone of this rule. The predicates themselves are NOT cloned.

clone_append(predicate_label, producer_pred, bin=False)¶: Returns a copy of this rule where ‘predicate_label’ is appended to the rule.

clone_negate(target_pred)¶: Returns a copy of this rule where ‘taget_pred’ is negated.

clone_swap_with_subclass(target_pred, child_pred_label)¶: Returns a copy of this rule where ‘target_pred’ is swapped for ‘child_pred_label’.

examples(positive_only=False)¶: Returns the covered examples.

property positives¶

precision()¶

rule_report(show_uris=False, latex=False)¶: Rule as string with some statistics.

static ruleset_examples_json(rules_per_target, show_uris=False)¶

static ruleset_report(rules, show_uris=False, latex=False, human=<function Rule.<lambda>>)¶

similarity(rule)¶: Calculates the similarity between this rule and ‘rule’.

size()¶: Returns the number of conjunts.

static to_json(rules_per_target, show_uris=False)¶

py3plex.algorithms.hedwig.core.settings module¶

Global settings file.

@author: anze.vavpetic@ijs.si

class py3plex.algorithms.hedwig.core.settings.Defaults¶

Bases: object

ADJUST = 'fwer'¶

ALPHA = 0.05¶

BEAM_SIZE = 20¶

COVERED = None¶

DEPTH = 5¶

FDR_Q = 0.05¶

FORMAT = 'n3'¶

LEARNER = 'heuristic'¶

LEAVES = False¶

MODE = 'subgroups'¶

NEGATIONS = False¶

NO_CACHE = False¶

OPTIMAL_SUBCLASS = False¶

OUTPUT = None¶

SCORE = 'lift'¶

SUPPORT = 0.1¶

TARGET = None¶

URIS = False¶

VERBOSE = False¶

py3plex.algorithms.hedwig.core.term_parsers module¶

py3plex.algorithms.hedwig.core.term_parsers.parse_gaf_file(gaf_mappings, whole_list_counts=False)¶

py3plex.algorithms.hedwig.core.term_parsers.read_termlist(terms)¶

py3plex.algorithms.hedwig.core.term_parsers.read_topology_mappings(mapping)¶

py3plex.algorithms.hedwig.core.term_parsers.read_uniprot_GO(filename, verbose=True)¶

Module contents¶

class py3plex.algorithms.hedwig.core.Example(id, label, score, annotations=[], weights={})¶

Bases: object

Represents an example with its score, label, id and annotations.

ClassLabeled = 'class'¶

Ranked = 'ranked'¶

class py3plex.algorithms.hedwig.core.UnaryPredicate(label, members, kb, producer_pred=None, custom_var_name=None, negated=False)¶

Bases: py3plex.algorithms.hedwig.core.predicate.Predicate

A unary predicate.

class py3plex.algorithms.hedwig.core.BinaryPredicate(label, pairs, kb, producer_pred=None)¶

Bases: py3plex.algorithms.hedwig.core.predicate.Predicate

A binary predicate.

class py3plex.algorithms.hedwig.core.Rule(kb, predicates=[], target=None)¶

Bases: object

Represents a rule, along with its description, examples and statistics.

clone()¶: Returns a clone of this rule. The predicates themselves are NOT cloned.

clone_append(predicate_label, producer_pred, bin=False)¶: Returns a copy of this rule where ‘predicate_label’ is appended to the rule.

clone_negate(target_pred)¶: Returns a copy of this rule where ‘taget_pred’ is negated.

clone_swap_with_subclass(target_pred, child_pred_label)¶: Returns a copy of this rule where ‘target_pred’ is swapped for ‘child_pred_label’.

examples(positive_only=False)¶: Returns the covered examples.

property positives¶

precision()¶

rule_report(show_uris=False, latex=False)¶: Rule as string with some statistics.

static ruleset_examples_json(rules_per_target, show_uris=False)¶

static ruleset_report(rules, show_uris=False, latex=False, human=<function Rule.<lambda>>)¶

similarity(rule)¶: Calculates the similarity between this rule and ‘rule’.

size()¶: Returns the number of conjunts.

static to_json(rules_per_target, show_uris=False)¶

class py3plex.algorithms.hedwig.core.ExperimentKB(triplets, score_fun, instances_as_leaves=True)¶

Bases: object

The knowledge base for one specific experiment.

add_sub_class(sub, obj)¶: Adds the resource ‘sub’ as a subclass of ‘obj’.

bits_to_indices(bits)¶: Converts the bitset to a set of indices.

get_domains(predicate)¶: Returns the bitsets for input and outputexamples of the binary predicate ‘predicate’.

get_empty_domain()¶: Returns a bitset covering no examples.

get_examples()¶: Returns all examples for this experiment.

get_full_domain()¶: Returns a bitset covering all examples.

get_members(predicate, bit=True)¶: Returns the examples for this predicate, either as a bitset or a set of ids.

get_reverse_members(predicate, bit=True)¶: Returns the examples for this predicate, either as a bitset or a set of ids.

get_root()¶: Root predicate, which covers all examples.

get_score(ex_idx)¶: Returns the score for example id ‘ex_idx’.

get_subclasses(predicate, producer_pred=None)¶: Returns a list of subclasses (as predicate objects) for ‘predicate’.

indices_to_bits(indices)¶: Converts the indices to a bitset.

is_discrete_target()¶

n_examples()¶: Returns the number of examples.

n_members(predicate)¶

super_classes(pred)¶: Returns all super classes of pred (with transitivity).

py3plex.algorithms.hedwig.core.convert_mapping_to_rdf(input_mapping_file, extract_subnode_info=False, split_node_by=':', keep_index=1, layer_type='uniprotkb', annotation_mapping_file='test.gaf', go_identifier='GO:', prepend_string=None)¶