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Added condition to handle empty eRegulons after build_grn #538

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Added condition to handle empty eRegulons after build_grn #538

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32 changes: 22 additions & 10 deletions src/scenicplus/cli/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -913,16 +913,28 @@ def infer_grn(
disable_tqdm=False,
seed=seed)

log.info("Formatting eGRN as table.")
eRegulon_metadata = _format_egrns(
eRegulons=eRegulons,
tf_to_gene=tf_to_gene)

log.info("Calculating triplet ranking.")
eRegulon_metadata = calculate_triplet_score(
cistromes=cistromes,
eRegulon_metadata=eRegulon_metadata,
ranking_db_fname=ranking_db_fname)
if eRegulons:
log.info("Formatting eGRN as table.")
eRegulon_metadata = _format_egrns(
eRegulons=eRegulons,
tf_to_gene=tf_to_gene
)
log.info("Calculating triplet ranking.")
eRegulon_metadata = calculate_triplet_score(
cistromes=cistromes,
eRegulon_metadata=eRegulon_metadata,
ranking_db_fname=ranking_db_fname
)
else:
Warning(
'No eRegulons were identified. Consider adjusting the thresholds to be less stringent, such as reducing the values for min_target_genes, rho_threshold, or min_regions_per_gene.'
)
cols = [
'Region', 'Gene', 'importance_R2G', 'rho_R2G importance_x_rho', 'importance_x_abs_rho', 'TF',
'is_extended', 'eRegulon_name', 'Gene_signature_name', 'Region_signature_name', 'importance_TF2G',
'regulation', 'rho_TF2G', 'triplet_rank'
]
eRegulon_metadata = pd.DataFrame(columns=cols)

log.info(f"Saving network to {eRegulon_out_fname.__str__()}")
eRegulon_metadata.to_csv(
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