biors-python
Python bindings for bio-rs via PyO3.
Installation
pip install biors
Requires Python 3.9+.
Quickstart
import json
import biors
fasta_text = (
">seq1\nACDEFGHIKLMNPQRSTVWY\n"
">seq2\nMKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCP\n"
)
# Parse FASTA text
records = biors.parse_fasta_records(fasta_text)
# Validate
report = biors.validate_fasta_input(fasta_text)
rna_report = biors.validate_fasta_input_with_kind(">rna\nACGUN\n", "rna")
print(f"Valid records: {report.valid_records}/{report.records}")
for record in report.sequences:
for issue in record.warnings:
print(f"{record.id}: ambiguous residue {issue.residue} at {issue.position}")
for issue in record.errors:
print(f"{record.id}: invalid residue {issue.residue} at {issue.position}")
# Tokenize
tokenized = biors.tokenize_fasta_records(fasta_text)
for t in tokenized:
print(t.id, t.alphabet, t.valid, t.tokens)
for issue in t.warnings + t.errors:
print(issue.residue, issue.position)
# Tokenize one in-memory sequence with a caller-provided ID
single = biors.tokenize_protein("ACDEFG", id="sample-001")
print(single.id, single.tokens)
# DNA/RNA use explicit tokenizer profiles.
dna = biors.tokenize_fasta_records(">dna\nACGT\n", profile="dna-iupac")
rna_workflow = biors.prepare_workflow_from_fasta(
">rna\nACGU\n",
max_length=8,
profile="rna-iupac",
)
# Build model input
model_input = biors.build_model_inputs_checked(
tokenized,
max_length=512,
pad_token_id=0,
padding="fixed_length",
)
for r in model_input.records:
print(r.id, r.input_ids, r.attention_mask)
# End-to-end workflow
output = biors.prepare_workflow_from_fasta(
fasta_text,
max_length=512,
pad_token_id=0,
padding="fixed_length",
)
print(f"Model ready: {output.model_ready}")
print(output.report_json)
# Validate a package on disk, including artifact paths and checksums.
package_report = json.loads(
biors.validate_package_manifest_file("./protein-package/manifest.json")
)
print(package_report["valid"])
validate_package_manifest(manifest_json) is field-only validation for an
in-memory manifest. Use validate_package_manifest_artifacts(manifest_json, base_dir) or validate_package_manifest_file(manifest_path) when package
files, checksums, and layout placement must be verified.
Errors raised by core parsing, model-input, and package helpers are
BioRsError values with stable code, message, and optional location
attributes, while still subclassing ValueError.
Development
Build locally with maturin:
cd crates/biors-python
maturin develop
pytest
License
MIT OR Apache-2.0
1 maintainer
Metadata
1 maintainer
Release files for biors 1.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| biors-1.0.0.tar.gz | 175.2 kB | Without provenance | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| biors-1.0.0-cp39-abi3-win_amd64.whl | CPython 3.9 | abi3 | Windows x86-64 | Details |
| biors-1.0.0-cp39-abi3-manylinux_2_34_x86_64.whl | CPython 3.9 | abi3 | Linux glibc 2.34+ x86-64 | Details |
| biors-1.0.0-cp39-abi3-macosx_11_0_arm64.whl | CPython 3.9 | abi3 | macOS 11.0+ ARM64 | Details |
Total release size: 1.8 MB
Release files / biors-1.0.0.tar.gz
| Download URL | biors-1.0.0.tar.gz |
|---|---|
| Size | 175.2 kB |
| Tags | Source |
|
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Release files / biors-1.0.0-cp39-abi3-win_amd64.whl
| Download URL | biors-1.0.0-cp39-abi3-win_amd64.whl |
|---|---|
| Size | 439.2 kB |
| Tags | CPython 3.9 Windows x86-64 abi3 |
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Release files / biors-1.0.0-cp39-abi3-manylinux_2_34_x86_64.whl
| Download URL | biors-1.0.0-cp39-abi3-manylinux_2_34_x86_64.whl |
|---|---|
| Size | 624.2 kB |
| Tags | CPython 3.9 Linux glibc 2.34+ x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
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| Uploaded via |
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|
Release files / biors-1.0.0-cp39-abi3-macosx_11_0_arm64.whl
| Download URL | biors-1.0.0-cp39-abi3-macosx_11_0_arm64.whl |
|---|---|
| Size | 559.6 kB |
| Tags | CPython 3.9 abi3 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
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