Gene Feature Attachment & CLI

Gene length and intron count are used for optional bias correction inside active_score.

# Use bundled tables
adata = scat.add_gene_features(adata, organism="mouse")  # or "human"

# or provide your own table
adata = scat.add_gene_features(adata, gene_features_path="my_features.parquet")

The package includes tables for mouse and human. Use organism="mouse" (default) or organism="human" when calling add_gene_features. For other species or custom annotations use the gene feature generator CLI.

Command-line interface

The only console script is the gene-feature table generator:

pip install "scatrans[gene_features]"
generate-gene-features --gtf /path/to/genes.gtf --output my_features.parquet --organism human

Works with 10x genes.gtf or GENCODE GTFs:

# Mouse
generate-gene-features --gtf /path/to/genes.gtf \
                       --output my_mouse_features.parquet \
                       --organism mouse

# Human (GENCODE or 10x)
generate-gene-features --gtf gencode.v49.primary_assembly.annotation.gtf \
                       --output human_GRCh38_2024A_gene_features.parquet \
                       --organism human

Then use it:

import scatrans as scat

adata = scat.add_gene_features(
    adata,
    gene_features_path="human_GRCh38_2024A_gene_features.parquet"
)

# bias correction will now be able to use length + intron_number
adata_res, significant, all_results = scat.active_score(adata, ...)

You can also call the generator programmatically:

from scatrans import generate_gene_features_from_gtf

df = generate_gene_features_from_gtf(
    "path/to/genes.gtf",
    output_name="my_custom_features.parquet",
    organism="human"
)

See also scat.list_available_gene_features() (for bundled tables) and the full signature of add_gene_features in the API Reference.

Tip: The generated parquet must contain a gene_name column (plus gene_length and intron_number). add_gene_features does a reindex on your adata.var_names.