Skip to content

Commit da10014

Browse files
committed
Updated README
1 parent c2efd91 commit da10014

1 file changed

Lines changed: 25 additions & 4 deletions

File tree

README.md

Lines changed: 25 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -12,9 +12,13 @@
1212

1313
## What is this?
1414

15-
`bbconf` is a configuration and management tool for BEDbase, facilitating the reading of configuration files,
16-
setting up connections to PostgreSQL, PEPhub, S3, and Qdrant databases, managing file paths, and storing transformer models.
17-
It formalizes communication pathways for pipelines and downstream tools, ensuring seamless interaction."
15+
`bbconf` is a configuration and data management library for the [BEDbase](https://bedbase.org) platform. It serves as the central backbone for all BEDbase tools and pipelines by:
16+
17+
- Reading and validating YAML configuration files
18+
- Setting up and managing connections to PostgreSQL, Qdrant, S3, and PEPHub
19+
- Loading ML models (Region2Vec, text embedders, sparse encoders, UMAP) used for BED file search
20+
- Providing high-level Python interfaces for querying and managing BED files and BED sets
21+
- Exposing a unified `BedBaseAgent` object that all downstream tools use to interact with the platform
1822

1923
---
2024

@@ -28,10 +32,27 @@ It formalizes communication pathways for pipelines and downstream tools, ensurin
2832

2933
To install `bbclient` use this command:
3034
```
31-
pip install bbclient
35+
pip install bbconf
3236
```
3337
or install the latest version from the GitHub repository:
3438
```
3539
pip install git+https://github.com/databio/bbconf.git
3640
```
3741

42+
43+
## Quick start
44+
45+
```python
46+
from bbconf import BedBaseAgent
47+
48+
agent = BedBaseAgent(config="config.yaml")
49+
50+
# Access submodules
51+
agent.bed # BED file operations
52+
agent.bedset # BED set operations
53+
agent.objects # Generic object/file operations
54+
55+
# Get platform statistics
56+
stats = agent.get_stats()
57+
print(stats.bedfiles_number, stats.bedsets_number)
58+
```

0 commit comments

Comments
 (0)