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fix(cli): 🐛 Implemented an overflow-safe fix for the sigmoid calculation on postProbEffect #108

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Merged
visze merged 1 commit into from
May 7, 2026
Merged

fix(cli): 🐛 Implemented an overflow-safe fix for the sigmoid calculation on postProbEffect #108

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12 changes: 10 additions & 2 deletions src/mpralib/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,14 @@
pd.options.mode.copy_on_write = True


def _safe_sigmoid(x: float) -> float:
"""Compute sigmoid while safely handling extreme values."""
try:
return math.exp(x) / (1 + math.exp(x))
except OverflowError:
return 1.0 if x > 0 else 0.0


@click.group(help="Command line interface of MPRAlib, a library for MPRA data analysis.")
def cli() -> None:
pass
Expand Down Expand Up @@ -993,7 +1001,7 @@ def get_reporter_variants(
},
inplace=True,
)
df["postProbEffect"] = df["B"].apply(lambda x: math.exp(x) / (1 + math.exp(x)))
df["postProbEffect"] = df["B"].apply(_safe_sigmoid)
df["variant_id"] = df.index

def _extract_allele_or_zero(variant_id, idx):
Expand Down Expand Up @@ -1270,7 +1278,7 @@ def get_reporter_genomic_variants(
},
inplace=True,
)
df["postProbEffect"] = df["B"].apply(lambda x: math.exp(x) / (1 + math.exp(x)))
df["postProbEffect"] = df["B"].apply(_safe_sigmoid)
df["variant_id"] = df.index

def _extract_allele_or_zero(variant_id, idx):
Expand Down
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