def set_sister_species_sentence(dm: WBDataManager,
conf_parser: GenedescConfigParser,
sister_sp_fullname, sister_df: WBDataManager,
species, organism, gene_desc: GeneDescription,
gene: Gene):
best_ortholog = dm.get_best_orthologs_for_gene(
gene_desc.gene_id,
orth_species_full_name=[sister_sp_fullname],
sister_species_data_fetcher=sister_df,
ecode_priority_list=[
"EXP", "IDA", "IPI", "IMP", "IGI", "IEP", "HTP", "HDA", "HMP",
"HGI", "HEP"
])[0][0]
if not best_ortholog[0].startswith("WB:"):
best_ortholog[0] = "WB:" + best_ortholog[0]
sister_sentences_generator = OntologySentenceGenerator(
gene_id=best_ortholog[0],
module=Module.GO,
data_manager=sister_df,
config=conf_parser,
humans=sister_sp_fullname == "H**o sapiens",
limit_to_group="EXPERIMENTAL")
sister_sp_module_sentences = sister_sentences_generator.get_module_sentences(
aspect='P',
qualifier="involved_in",
merge_groups_with_same_prefix=True,
keep_only_best_group=True)
if sister_sp_module_sentences.contains_sentences():
gene_desc.set_or_extend_module_description_and_final_stats(
module=Module.SISTER_SP,
description="in " +
species[species[organism]["main_sister_species"]]["name"] + ", " +
best_ortholog[1] + " " +
sister_sp_module_sentences.get_description())
def get_best_orthologs_and_sentence(dm: WBDataManager,
orth_fullnames: List[str],
gene_desc: GeneDescription,
human_genes_props, api_manager,
config: GenedescConfigParser):
best_orthologs, selected_orth_name = dm.get_best_orthologs_for_gene(
gene_desc.gene_id, orth_species_full_name=orth_fullnames)
selected_orthologs = []
orth_sent = ''
if best_orthologs:
gene_desc.stats.set_best_orthologs = [
orth[0] for orth in best_orthologs
]
if len(orth_fullnames) == 1 and orth_fullnames[0] == "H**o sapiens":
sel_orthologs, orth_sent = generate_ortholog_sentence_wormbase_human(
best_orthologs, human_genes_props, config=config)
selected_orthologs = [
orth for orth in best_orthologs
if orth[1].upper() in sel_orthologs
]
else:
orth_sent = generate_ortholog_sentence_wormbase_non_c_elegans(
best_orthologs,
selected_orth_name,
api_manager=api_manager,
config=config)
return selected_orthologs, orth_sent
def set_orthology_sentence(dm: WBDataManager, orth_fullnames: List[str], gene_desc: GeneDescription,
human_genes_props, api_manager):
best_orthologs, selected_orth_name = dm.get_best_orthologs_for_gene(gene_desc.gene_id,
orth_species_full_name=orth_fullnames)
selected_orthologs = []
if best_orthologs:
gene_desc.stats.set_best_orthologs = [orth[0] for orth in best_orthologs]
if len(orth_fullnames) == 1 and orth_fullnames[0] == "H**o sapiens":
sel_orthologs, orth_sent = generate_ortholog_sentence_wormbase_human(best_orthologs, human_genes_props)
selected_orthologs = [orth for orth in best_orthologs if orth[1] in sel_orthologs]
else:
orth_sent = generate_ortholog_sentence_wormbase_non_c_elegans(best_orthologs, selected_orth_name,
api_manager=api_manager)
gene_desc.set_or_extend_module_description_and_final_stats(module=Module.ORTHOLOGY, description=orth_sent)
return selected_orthologs