biotailor 0.1.1

Python SDK for the Biotailor bioinformatics pipeline platform

biotailor

Python SDK for the Biotailor bioinformatics pipeline platform.

Installation

pip install biotailor

Quickstart

import os
from biotailor import BiotailorClient, Pipeline

# 1. Create a client with your API key (get one at https://biotailor.com)
client = BiotailorClient(
    api_key=os.environ["BIOTAILOR_API_KEY"],
    base_url="https://api.biotailor.org",
)

# 2. Pick a bioinformatics tool
fastp = client.get_tool("fastp")

# 3. Build a quality-control pipeline
pipeline = (
    Pipeline(name="demo-fastp", tool=fastp)
    .set_pair_end(False)
    .set_input("--in1", "examples/reads.fastq")
    .set_param("--qualified_quality_phred", 20)
    .set_param("--length_required", 30)
)

# 4. Run and wait for results
job = client.run_and_wait(pipeline, output_dir="outputs/")
print(f"Done! Status: {job.job_status.value}")

Development

# Install in dev mode
pip install -e ".[dev]"

# Run tests
pytest tests/ -v

# Lint
ruff check src/ tests/