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
pip install roxylib
# or with uv:
uv add roxylib
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.pyfor direct descriptor use from Pythonexamples/configured_descriptors.pyfor parameterized descriptor instancesexamples/cli_roundtrip.pyfor 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 |
| 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
uv run pytest -q
uv run task lint
uv run roxy --help
Related Projects
- Sylphy — sequence encoders and pretrained model embeddings
1 maintainer
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