Roxy

Classical protein sequence descriptors for machine learning.

Roxy computes classical numerical descriptors from amino-acid sequences and returns tabular features as polars.DataFrame objects.

Install

Not yet published on PyPI. Install directly from GitHub:

pip install git+https://github.com/kren-ai-lab/roxy.git
# or with uv:
uv add git+https://github.com/kren-ai-lab/roxy.git

Quickstart

from roxy import read_fasta, DESCRIPTOR_REGISTRY

# Load sequences from FASTA
records = read_fasta("sequences.fasta")  # [(id, seq), ...]
sequences = [seq for _, seq in records]
ids = [seq_id for seq_id, _ in records]

descriptor = DESCRIPTOR_REGISTRY["aac"]()
features = descriptor.compute(sequences, ids=ids)  # polars.DataFrame

For direct Python use, descriptors are importable by family:

from roxy.descriptors.aaindex import AAIndexDescriptor
from roxy.descriptors.composition import KmerFullAlphabetDescriptor
from roxy.descriptors.physicochemical import ChargeDescriptor

kmer = KmerFullAlphabetDescriptor(k=2)
aaindex = AAIndexDescriptor()
charge = ChargeDescriptor()

kmer_features = kmer.compute(["ACDEFGHIK"])
aaindex_features = aaindex.compute(["ACDEFGHIK"])
charge_features = charge.compute(["ACDEFGHIK"])

CLI

roxy --help
roxy --version

# List and inspect descriptors
roxy list
roxy list --family composition
roxy describe aac

# Compute descriptors from FASTA, CSV, or Parquet input
roxy compute sequences.fasta -d aac -d charge -o features.csv
roxy compute sequences.fasta -f composition -o composition.parquet
roxy compute sequences.csv -d aac --seq-col sequence --id-col id -o features.csv
roxy compute sequences.fasta --all -o all_features.parquet

# Generate and use a YAML config with descriptor parameters
roxy init-config -d aac -d charge -o roxy.yaml
roxy init-config -f composition -o composition.yaml
roxy init-config --all -o all_descriptors.yaml
roxy compute sequences.fasta --config roxy.yaml -o configured_features.csv

roxy compute requires exactly one descriptor selector: --config, --all, --descriptor/-d, or --family/-f. CSV and Parquet inputs use sequence as the default sequence column; pass --seq-col and --id-col when needed.

Examples

The repository ships a few plain Python scripts under examples/:

• examples/basic_api.py for direct descriptor use from Python
• examples/configured_descriptors.py for parameterized descriptor instances
• examples/cli_roundtrip.py for an end-to-end CLI config and compute flow

Run them with:

bash examples/run_ci_examples.sh

Descriptor Families

Registry keys are the names used by roxy compute -d, config files, and output column prefixes.

Family	Descriptor keys
aaindex	aaindex
autocorrelation	autocorrelation
complexity	entropy_complexity, local_repetition, run_blockiness
composition	aac, compositional_bias, dpc, grouped, kmer_full_alphabet, reduced_kmer
ctd	ctd_classic, distribution
hybrid	family_summary
motif	functional_residue_content, pattern, spacing, user_regex
physicochemical	charge, global_basic, hydrophobicity, order_disorder, structural_propensity
positional	normalized, sliding_window, terminal
pseudo	pseaac, qso, sequence_order

Development

uv sync --all-extras
uv run pytest -q
uv run task lint
uv run roxy --help

Related Projects

• Sylphy — sequence encoders and pretrained model embeddings