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fix(cli): 🐛 supportig 0 alleles #112

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Merged
visze merged 1 commit into from
Jun 25, 2026
Merged

fix(cli): 🐛 supportig 0 alleles #112

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34 changes: 11 additions & 23 deletions src/mpralib/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1004,17 +1004,6 @@ def get_reporter_variants(
df["postProbEffect"] = df["B"].apply(_safe_sigmoid)
df["variant_id"] = df.index

def _extract_allele_or_zero(variant_id, idx):
if pd.isna(variant_id):
return 0
parts = str(variant_id).split(":")
if len(parts) <= idx:
return 0
allele = parts[idx]
if pd.isna(allele) or allele == "":
return 0
return allele

df["refAllele"] = df["variant_id"].apply(lambda x: _extract_allele_or_zero(x, 2))
df["altAllele"] = df["variant_id"].apply(lambda x: _extract_allele_or_zero(x, 3))
df["variantPos"] = df["variantPos"].astype(int)
Expand Down Expand Up @@ -1281,21 +1270,10 @@ def get_reporter_genomic_variants(
df["postProbEffect"] = df["B"].apply(_safe_sigmoid)
df["variant_id"] = df.index

def _extract_allele_or_zero(variant_id, idx):
if pd.isna(variant_id):
return 0
parts = str(variant_id).split(":")
if len(parts) <= idx:
return 0
allele = parts[idx]
if pd.isna(allele) or allele == "":
return 0
return allele

df["refAllele"] = df["variant_id"].apply(lambda x: _extract_allele_or_zero(x, 2))
df["altAllele"] = df["variant_id"].apply(lambda x: _extract_allele_or_zero(x, 3))
df["start"] = df["variant_id"].apply(lambda x: x.split(":")[1]).astype(int)
df["end"] = df["start"] + df["refAllele"].apply(lambda x: len(x)).astype(int)
df["end"] = df["start"] + df["refAllele"].apply(lambda x: len(str(x)) if isinstance(x, str) else 1).astype(int)

map = chromosome_map()
map = map[map["release"] == reference]
Expand Down Expand Up @@ -1342,6 +1320,16 @@ def _get_chr(map: pd.DataFrame, variant_id: str, logger: logging.Logger) -> str
return None


def _extract_allele_or_zero(variant_id: str, idx: int) -> str | int:
parts = variant_id.split(":")
if len(parts) <= idx:
return 0
allele = parts[idx]
if pd.isna(allele) or allele == "":
return 0
return allele


@cli.group(help="Plotting functions.")
def plot() -> None:
pass
Expand Down
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