infer_sex (Python)

Pythonic port of SauersML/infer_sex. Counts heterozygous calls per chromosome region and applies a linear decision boundary on (x_autosome_het_ratio, y_genome_density) to call genetic sex. The algorithm + every numeric constant are kept byte- identical to the Rust crate.

from infer_sex import SexInferer, platform_from_bim

inferer = SexInferer(
    build="hg38",
    platform=platform_from_bim("/data/cohort.bim", build="hg38"),
)

# Pick your input — they're all type-checked and return the same shape:
result = inferer.infer_from_vcf("/data/sample.vcf.gz")
# or  inferer.infer_from_plink("/data/cohort")
# or  inferer.infer_from_records([("X", 100_000_000, True), ...])
# or  inferer.infer_from_arrays(chrom_codes, positions, is_het)

print(result.final_call)   # InferredSex.MALE / .FEMALE / .INDETERMINATE
print(result.report.composite_sex_index)

Install

pip install infer_sex

Pure Python + numpy. No Rust toolchain required.

Platform definitions

The algorithm normalises observed counts by the attempted counts on the platform — pass them in via PlatformDefinition. Two helpers compute them for you in one call:

from infer_sex import platform_from_bim, platform_from_vcf

platform = platform_from_bim("/data/cohort.bim", build="hg38")
platform = platform_from_vcf("/data/cohort.vcf.gz", build="hg38")

These walk the file once, counting autosomal rows and Y-non-PAR rows. Everything else (X, Y-PAR, MT, alt contigs) is ignored — exactly the locus set the inference algorithm uses for normalisation.

If you already know the counts (e.g. from a manifest), construct PlatformDefinition directly:

from infer_sex import PlatformDefinition

platform = PlatformDefinition(
    n_attempted_autosomes=2_000,
    n_attempted_y_nonpar=1_000,
)

Shortcuts: pass what you already know

infer_sex never touches the network. Skip build detection by passing build= directly. Use custom decision thresholds (e.g. one fit on your own labelled data) via DecisionThresholds:

from infer_sex import DecisionThresholds

inferer = SexInferer(
    build="hg38",
    platform=PlatformDefinition(...),
    thresholds=DecisionThresholds(slope=0.30, intercept=0.25),
)

Inputs

• infer_from_vcf(path) — .vcf / .vcf.gz. Multi-sample files default to the first column with a UserWarning; pass sample= to pick by ID (str) or 0-based index (int).
• infer_from_plink(prefix) — variant-major .bed/.bim/.fam. Pass sample= to pick a specific row of the FAM (string IID/FID or 0-based index). Reads via np.memmap; biobank-scale .beds are fine.
• infer_from_records(iterable) — accepts (chrom, pos, is_het) triples. Useful when reading from a custom source.
• infer_from_arrays(chrom, pos, is_het) — parallel numpy arrays; ~10× faster than infer_from_records for the same data.

Missing genotypes (./. in VCF, 0b01 in PLINK) are dropped — they don't count toward the denominator, matching the Rust crate.

Streaming API

SexInferenceAccumulator is the streaming primitive:

acc = inferer.accumulator()
for chrom, pos, is_het in my_stream:
    acc.add(chrom, pos, is_het)
# bulk path:
acc.add_batch(chrom_array, pos_array, is_het_array)
# any time:
print(acc.snapshot())       # raw counts, no classification
result = acc.finish()        # full inference; does not consume the accumulator

Results

result.final_call           # InferredSex enum
result.is_male / .is_female / .is_indeterminate
result.report.y_genome_density          # Optional[float]
result.report.x_autosome_het_ratio      # Optional[float]
result.report.composite_sex_index       # Optional[float]
result.report.auto_valid_count          # int (and many more counts)
result.report.as_dict()                  # plain dict, JSON-ready

Errors

• InvalidPlatformCounts — the PlatformDefinition is unusable (e.g. zero autosomes).
• ObservedExceedsAttempted — more observations than the platform claims (your platform definition doesn't match the input stream).

Both subclass InferenceError.

Cross-language guarantee

Every PAR/non-PAR coordinate, the 1e-9 epsilon, the default DecisionThresholds(slope=0.3566, intercept=0.2738), and the classification formula are kept byte-identical to src/lib.rs in this same repo. Calls match across languages — feed the same variant stream to the Rust accumulator and the Python SexInferer and you get the same InferredSex.