bbconf

BEDBASE project configuration package (agent)

What is this?

bbconf is a configuration and data management library for the BEDbase platform. It serves as the central backbone for all BEDbase tools and pipelines by:

• Reading and validating YAML configuration files
• Setting up and managing connections to PostgreSQL, Qdrant, S3, and PEPHub
• Loading ML models (Region2Vec, text embedders, sparse encoders, UMAP) used for BED file search
• Providing high-level Python interfaces for querying and managing BED files and BED sets
• Exposing a unified BedBaseAgent object that all downstream tools use to interact with the platform

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Documentation: https://docs.bedbase.org/bedboss

Source Code: https://github.com/databio/bbconf

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Installation

To install bbclient use this command:

pip install bbconf

or install the latest version from the GitHub repository:

pip install git+https://github.com/databio/bbconf.git

Quick start

from bbconf import BedBaseAgent

agent = BedBaseAgent(config="config.yaml")

# Access submodules
agent.bed        # BED file operations
agent.bedset     # BED set operations
agent.objects    # Generic object/file operations

# Get platform statistics
stats = agent.get_stats()
print(stats.bedfiles_number, stats.bedsets_number)