def set_expression_module(df: DataManager, conf_parser: GenedescConfigParser, gene_desc: GeneDescription, gene: Gene):
expr_sentence_generator = OntologySentenceGenerator(gene_id=gene.id, module=Module.EXPRESSION, data_manager=df,
config=conf_parser)
expression_module_sentences = expr_sentence_generator.get_module_sentences(
aspect='A', qualifier="Verified", merge_groups_with_same_prefix=True, keep_only_best_group=False)
gene_desc.set_or_extend_module_description_and_final_stats(module_sentences=expression_module_sentences,
module=Module.EXPRESSION)
gene_desc.set_or_update_initial_stats(module=Module.EXPRESSION, sent_generator=expr_sentence_generator,
module_sentences=expression_module_sentences)
def set_disease_module(df: DataManager, conf_parser: GenedescConfigParser, gene_desc: GeneDescription, gene: Gene,
human: bool = False):
do_sentence_exp_generator = OntologySentenceGenerator(gene_id=gene.id,
module=Module.DO_EXPERIMENTAL, data_manager=df,
config=conf_parser, limit_to_group="EXPERIMENTAL",
humans=human)
disease_exp_module_sentences = do_sentence_exp_generator.get_module_sentences(
aspect='D', merge_groups_with_same_prefix=True, keep_only_best_group=False)
gene_desc.set_or_extend_module_description_and_final_stats(module=Module.DO_EXPERIMENTAL,
module_sentences=disease_exp_module_sentences)
do_sentence_bio_generator = OntologySentenceGenerator(gene_id=gene.id, module=Module.DO_BIOMARKER,
data_manager=df, config=conf_parser,
limit_to_group="BIOMARKER", humans=human)
disease_bio_module_sentences = do_sentence_bio_generator.get_module_sentences(
aspect='D', merge_groups_with_same_prefix=True, keep_only_best_group=False)
gene_desc.set_or_extend_module_description_and_final_stats(module=Module.DO_BIOMARKER,
module_sentences=disease_bio_module_sentences)
do_via_orth_sentence_generator = OntologySentenceGenerator(
gene_id=gene.id, module=Module.DO_ORTHOLOGY, data_manager=df, config=conf_parser, humans=human)
disease_via_orth_module_sentences = do_via_orth_sentence_generator.get_module_sentences(
aspect='D', merge_groups_with_same_prefix=True, keep_only_best_group=False)
gene_desc.set_or_extend_module_description_and_final_stats(module=Module.DO_ORTHOLOGY,
module_sentences=disease_via_orth_module_sentences)
gene_desc.set_or_update_initial_stats(module=Module.DO_EXPERIMENTAL, sent_generator=do_sentence_exp_generator,
module_sentences=disease_exp_module_sentences)
gene_desc.set_or_update_initial_stats(module=Module.DO_BIOMARKER, sent_generator=do_sentence_bio_generator,
module_sentences=disease_bio_module_sentences)
gene_desc.set_or_update_initial_stats(module=Module.DO_ORTHOLOGY, sent_generator=do_via_orth_sentence_generator,
module_sentences=disease_via_orth_module_sentences)
def set_gene_ontology_module(dm: DataManager, conf_parser: GenedescConfigParser, gene_desc: GeneDescription,
gene: Gene):
go_sent_generator_exp = OntologySentenceGenerator(gene_id=gene.id, module=Module.GO, data_manager=dm,
config=conf_parser, limit_to_group="EXPERIMENTAL")
go_sent_generator = OntologySentenceGenerator(gene_id=gene.id, module=Module.GO, data_manager=dm,
config=conf_parser)
# Generate sentences with experimental annotations only
func_module_sentences_contributes_to = go_sent_generator_exp.get_module_sentences(
aspect='F', qualifier='contributes_to', merge_groups_with_same_prefix=True, keep_only_best_group=True)
func_module_sentences_noq = go_sent_generator_exp.get_module_sentences(
aspect='F', qualifier='', merge_groups_with_same_prefix=True, keep_only_best_group=True)
func_module_sentences_enables = go_sent_generator_exp.get_module_sentences(
aspect='F', qualifier='enables', merge_groups_with_same_prefix=True, keep_only_best_group=True)
# If experimental sentences are all empty, generate sentences with all annotations
if not func_module_sentences_contributes_to.contains_sentences() and \
not func_module_sentences_noq.contains_sentences() and \
not func_module_sentences_enables.contains_sentences():
func_module_sentences_contributes_to = go_sent_generator.get_module_sentences(
aspect='F', qualifier='contributes_to', merge_groups_with_same_prefix=True, keep_only_best_group=True)
func_module_sentences_noq = go_sent_generator.get_module_sentences(
aspect='F', qualifier='', merge_groups_with_same_prefix=True, keep_only_best_group=True)
func_module_sentences_enables = go_sent_generator.get_module_sentences(
aspect='F', qualifier='enables', merge_groups_with_same_prefix=True, keep_only_best_group=True)
gene_desc.set_or_extend_module_description_and_final_stats(module_sentences=func_module_sentences_noq,
module=Module.GO_FUNCTION)
gene_desc.set_or_extend_module_description_and_final_stats(module_sentences=func_module_sentences_enables,
module=Module.GO_FUNCTION)
gene_desc.set_or_extend_module_description_and_final_stats(module_sentences=func_module_sentences_contributes_to,
module=Module.GO_FUNCTION)
proc_module_sentences_noq = go_sent_generator_exp.get_module_sentences(
aspect='P', qualifier='', merge_groups_with_same_prefix=True, keep_only_best_group=True)
proc_module_sentences_inv = go_sent_generator_exp.get_module_sentences(
aspect='P', qualifier='involved_in', merge_groups_with_same_prefix=True, keep_only_best_group=True)
proc_module_sentences_acts_pos = go_sent_generator_exp.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_positive_effect', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
proc_module_sentences_acts_neg = go_sent_generator_exp.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_negative_effect', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
proc_module_sentences_acts_with_pos = go_sent_generator_exp.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_or_within_positive_effect', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
proc_module_sentences_acts_with_neg = go_sent_generator_exp.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_or_within_negative_effect', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
proc_module_sentences_acts_with = go_sent_generator_exp.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_or_within', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
if not proc_module_sentences_noq.contains_sentences() and \
not proc_module_sentences_inv.contains_sentences() and \
not proc_module_sentences_acts_pos.contains_sentences() and \
not proc_module_sentences_acts_neg.contains_sentences() and \
not proc_module_sentences_acts_with_pos.contains_sentences() and \
not proc_module_sentences_acts_with_neg.contains_sentences() and \
not proc_module_sentences_acts_with.contains_sentences():
proc_module_sentences_noq = go_sent_generator.get_module_sentences(
aspect='P', qualifier='', merge_groups_with_same_prefix=True, keep_only_best_group=True)
proc_module_sentences_inv = go_sent_generator.get_module_sentences(
aspect='P', qualifier='involved_in', merge_groups_with_same_prefix=True, keep_only_best_group=True)
proc_module_sentences_acts_pos = go_sent_generator.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_positive_effect', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
proc_module_sentences_acts_neg = go_sent_generator.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_negative_effect', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
proc_module_sentences_acts_with_pos = go_sent_generator.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_or_within_positive_effect', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
proc_module_sentences_acts_with_neg = go_sent_generator.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_or_within_negative_effect', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
proc_module_sentences_acts_with = go_sent_generator.get_module_sentences(
aspect='P', qualifier='acts_upstream_of_or_within', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=proc_module_sentences_noq, module=Module.GO_PROCESS)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=proc_module_sentences_inv, module=Module.GO_PROCESS)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=proc_module_sentences_acts_pos, module=Module.GO_PROCESS)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=proc_module_sentences_acts_neg, module=Module.GO_PROCESS)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=proc_module_sentences_acts_with_pos, module=Module.GO_PROCESS)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=proc_module_sentences_acts_with_neg, module=Module.GO_PROCESS)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=proc_module_sentences_acts_with, module=Module.GO_PROCESS)
comp_module_sentence_colocalizes_with = go_sent_generator_exp.get_module_sentences(
aspect='C', qualifier='colocalizes_with', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
comp_module_sentences_noq = go_sent_generator_exp.get_module_sentences(
aspect='C', qualifier='', merge_groups_with_same_prefix=True, keep_only_best_group=True)
comp_module_sentences_located = go_sent_generator_exp.get_module_sentences(
aspect='C', qualifier='located_in', merge_groups_with_same_prefix=True, keep_only_best_group=True)
comp_module_sentences_part = go_sent_generator_exp.get_module_sentences(
aspect='C', qualifier='part_of', merge_groups_with_same_prefix=True, keep_only_best_group=True)
comp_module_sentences_active = go_sent_generator_exp.get_module_sentences(
aspect='C', qualifier='is_active_in', merge_groups_with_same_prefix=True, keep_only_best_group=True)
if not comp_module_sentence_colocalizes_with.contains_sentences() and \
not comp_module_sentences_noq.contains_sentences() and \
not comp_module_sentences_located.contains_sentences() and \
not comp_module_sentences_part.contains_sentences() and \
not comp_module_sentences_active.contains_sentences():
comp_module_sentence_colocalizes_with = go_sent_generator.get_module_sentences(
aspect='C', qualifier='colocalizes_with', merge_groups_with_same_prefix=True,
keep_only_best_group=True)
comp_module_sentences_noq = go_sent_generator.get_module_sentences(
aspect='C', qualifier='', merge_groups_with_same_prefix=True, keep_only_best_group=True)
comp_module_sentences_located = go_sent_generator.get_module_sentences(
aspect='C', qualifier='located_in', merge_groups_with_same_prefix=True, keep_only_best_group=True)
comp_module_sentences_part = go_sent_generator.get_module_sentences(
aspect='C', qualifier='part_of', merge_groups_with_same_prefix=True, keep_only_best_group=True)
comp_module_sentences_active = go_sent_generator.get_module_sentences(
aspect='C', qualifier='is_active_in', merge_groups_with_same_prefix=True, keep_only_best_group=True)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=comp_module_sentences_noq, module=Module.GO_COMPONENT)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=comp_module_sentences_located, module=Module.GO_COMPONENT)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=comp_module_sentences_part, module=Module.GO_COMPONENT)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=comp_module_sentences_active, module=Module.GO_COMPONENT)
gene_desc.set_or_extend_module_description_and_final_stats(module_sentences=comp_module_sentence_colocalizes_with,
module=Module.GO_COMPONENT)
gene_desc.set_or_update_initial_stats(module=Module.GO_FUNCTION, sent_generator=go_sent_generator,
module_sentences=func_module_sentences_contributes_to)
gene_desc.set_or_update_initial_stats(module=Module.GO_FUNCTION, sent_generator=go_sent_generator,
module_sentences=func_module_sentences_noq)
gene_desc.set_or_update_initial_stats(module=Module.GO_FUNCTION, sent_generator=go_sent_generator,
module_sentences=func_module_sentences_enables)
gene_desc.set_or_update_initial_stats(module=Module.GO_PROCESS, sent_generator=go_sent_generator,
module_sentences=proc_module_sentences_noq)
gene_desc.set_or_update_initial_stats(module=Module.GO_PROCESS, sent_generator=go_sent_generator,
module_sentences=proc_module_sentences_inv)
gene_desc.set_or_update_initial_stats(module=Module.GO_PROCESS, sent_generator=go_sent_generator,
module_sentences=proc_module_sentences_acts_pos)
gene_desc.set_or_update_initial_stats(module=Module.GO_PROCESS, sent_generator=go_sent_generator,
module_sentences=proc_module_sentences_acts_neg)
gene_desc.set_or_update_initial_stats(module=Module.GO_PROCESS, sent_generator=go_sent_generator,
module_sentences=proc_module_sentences_acts_with_pos)
gene_desc.set_or_update_initial_stats(module=Module.GO_PROCESS, sent_generator=go_sent_generator,
module_sentences=proc_module_sentences_acts_with_neg)
gene_desc.set_or_update_initial_stats(module=Module.GO_PROCESS, sent_generator=go_sent_generator,
module_sentences=proc_module_sentences_acts_with)
gene_desc.set_or_update_initial_stats(module=Module.GO_COMPONENT, sent_generator=go_sent_generator,
module_sentences=comp_module_sentence_colocalizes_with)
gene_desc.set_or_update_initial_stats(module=Module.GO_COMPONENT, sent_generator=go_sent_generator,
module_sentences=comp_module_sentences_noq)
gene_desc.set_or_update_initial_stats(module=Module.GO_COMPONENT, sent_generator=go_sent_generator,
module_sentences=comp_module_sentences_located)
gene_desc.set_or_update_initial_stats(module=Module.GO_COMPONENT, sent_generator=go_sent_generator,
module_sentences=comp_module_sentences_part)
gene_desc.set_or_update_initial_stats(module=Module.GO_COMPONENT, sent_generator=go_sent_generator,
module_sentences=comp_module_sentences_active)