mehari 0.45.0

Python bindings for the mehari variant annotator

mehari

Python bindings for the mehari Rust library.

Features

• Single variants: Annotate a single variant using a format string (chr:pos:ref:alt) or keyword arguments.
• Multiple variants (experimental): Evaluate the compound effect of multiple variants.
• DataFrames: Process batches of variants by passing a polars.DataFrame.
• LazyFrames: Support for polars.LazyFrame to process large datasets (like Parquet files) without loading everything into memory.

Usage

Initialize SeqvarsAnnotator with your transcript database (see mehari-data-tx) and a reference genome (FASTA, uncompressed, with index).

from mehari import SeqvarsAnnotator

annotator = SeqvarsAnnotator(
    transcript_db_paths=["path/to/txs.bin.zst"],
    reference_path="path/to/reference.fa"
)

To annotate a single variant either use colon separated format string or keyword arguments:

result1 = annotator.annotate("17:41197701:G:C")
result2 = annotator.annotate(chromosome="3", position=193332511, reference="G", alternative="T")

To annotate multiple phased variants together as a single compound event (Experimental):

Note: Mehari does not infer phasing. When using annotate_multiple, mehari assumes all provided variants are on the same chromosome, exist on the same haplotype, and do not overlap.

result1 = annotator.annotate_multiple(["1:37799635:TA:A", "1:37799639:C:CG"])

result2 = annotator.annotate_multiple([
    {"chromosome": "1", "position": 37799635, "reference": "TA", "alternative": "A"},
    {"chromosome": "1", "position": 37799639, "reference": "C", "alternative": "CG"}
])

To annotate a batch of variants, pass a polars.DataFrame or polars.LazyFrame.

import polars as pl

df = pl.DataFrame(
    {
        "chromosome": ["17", "3"],
        "position": [41197701, 193332511],
        "reference": ["G", "G"],
        "alternative": ["C", "T"],
    },
    schema={
        "chromosome": pl.Categorical, "position": pl.Int32,
        "reference": pl.String, "alternative": pl.String
    }
)

annotated_df = annotator.annotate(df)

Schemas and types

Enums

Mehari exports its internal enums to Python so you can use them for filtering or comparisons:

from mehari import ConsequenceEnum, ImpactEnum

DataFrame Schema

When annotating a DataFrame or LazyFrame, mehari appends an "annotation" column. This column is a polars List(Struct) with the following fields:

• allele: String
• consequences: List(ConsequenceEnum)
• putative_impact: ImpactEnum
• gene_symbol: String
• gene_id: String
• feature_type: String
• feature_id: String
• feature_biotype: List(String)
• feature_tags: List(String)
• rank: Struct(ord: Int32, total: Int32)
• cdna_pos: Struct(ord: Int32, total: Int32)
• cds_pos: Struct(ord: Int32, total: Int32)
• protein_pos: Struct(ord: Int32, total: Int32)
• hgvs_g: String
• hgvs_n: String
• hgvs_c: String
• hgvs_p: String
• distance: Int32
• strand: Int32
• messages: List(String)

Building a transcript database

To build a transcript database, you can use the build_transcript_db function:

from mehari import build_transcript_db
build_transcript_db(
    assembly="grch38",
    annotation=["grch38.gff.gz"],
    transcript_sequences="grch38.fasta",
    transcript_source="ensembl",
    output="grch38.bin.zst"
)

This may take a while (several minutes for GRCh38 + Ensembl).