def set_disease_module(df: DataManager,
conf_parser: GenedescConfigParser,
gene_desc: GeneDescription,
gene: Gene,
orthologs_key_diseases=None,
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(
config=conf_parser,
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(
config=conf_parser,
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(
config=conf_parser,
aspect='D',
merge_groups_with_same_prefix=True,
keep_only_best_group=False,
high_priority_term_ids=orthologs_key_diseases)
gene_desc.set_or_extend_module_description_and_final_stats(
module=Module.DO_ORTHOLOGY,
module_sentences=disease_via_orth_module_sentences)
gene_desc.set_initial_stats(module=Module.DO_EXPERIMENTAL,
sentence_generator=do_sentence_exp_generator)
gene_desc.set_initial_stats(module=Module.DO_BIOMARKER,
sentence_generator=do_sentence_bio_generator)
gene_desc.set_initial_stats(
module=Module.DO_ORTHOLOGY,
sentence_generator=do_via_orth_sentence_generator)
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)
contributes_to_module_sentences = go_sent_generator.get_module_sentences(
config=conf_parser,
aspect='F',
qualifier='contributes_to',
merge_groups_with_same_prefix=True,
keep_only_best_group=True)
if contributes_to_module_sentences.contains_sentences():
func_module_sentences = go_sent_generator_exp.get_module_sentences(
config=conf_parser,
aspect='F',
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, module=Module.GO_FUNCTION)
else:
func_module_sentences = go_sent_generator.get_module_sentences(
config=conf_parser,
aspect='F',
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, module=Module.GO_FUNCTION)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=contributes_to_module_sentences,
module=Module.GO_FUNCTION)
proc_module_sentences = go_sent_generator.get_module_sentences(
config=conf_parser,
aspect='P',
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, module=Module.GO_PROCESS)
colocalizes_with_module_sentences = go_sent_generator.get_module_sentences(
config=conf_parser,
aspect='C',
qualifier='colocalizes_with',
merge_groups_with_same_prefix=True,
keep_only_best_group=True)
if colocalizes_with_module_sentences.contains_sentences():
comp_module_sentences = go_sent_generator_exp.get_module_sentences(
config=conf_parser,
aspect='C',
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, module=Module.GO_COMPONENT)
else:
comp_module_sentences = go_sent_generator.get_module_sentences(
config=conf_parser,
aspect='C',
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, module=Module.GO_COMPONENT)
gene_desc.set_or_extend_module_description_and_final_stats(
module_sentences=colocalizes_with_module_sentences,
module=Module.GO_COMPONENT)
gene_desc.set_initial_stats(
module=Module.GO_FUNCTION,
sentence_generator=go_sent_generator,
sentence_generator_exp_only=go_sent_generator_exp)
gene_desc.set_initial_stats(
module=Module.GO_PROCESS,
sentence_generator=go_sent_generator,
sentence_generator_exp_only=go_sent_generator_exp)
gene_desc.set_initial_stats(
module=Module.GO_COMPONENT,
sentence_generator=go_sent_generator,
sentence_generator_exp_only=go_sent_generator_exp)