RefgetDBAgent Tutorial¶

This tutorial shows you how to use RefgetDBAgent to manage a PostgreSQL database of sequence collections for building a seqcol API server.

Learning objectives

• Connect to a PostgreSQL database with RefgetDBAgent
• List and retrieve sequence collections
• Compare sequence collections
• Use specialized sub-agents for different operations

Prerequisites¶

This tutorial requires a running PostgreSQL database. Set up environment variables before running:

export POSTGRES_HOST=localhost
export POSTGRES_DB=refget
export POSTGRES_USER=postgres
export POSTGRES_PASSWORD=yourpassword

Or use the demo setup:

cd repos/refget
bash deployment/demo_up.sh  # Starts postgres + loads demo data

Note

For most users, the CLI (refget admin) or RefgetStore (local file-based storage) are simpler alternatives. Use RefgetDBAgent when you need direct database access for building a seqcol API server.

In [1]:

# Initialize the database agent
# Requires POSTGRES_* environment variables to be set
from refget.agents import RefgetDBAgent

agent = RefgetDBAgent()
print(f"Connected to database via: {agent.engine}")

# Initialize the database agent # Requires POSTGRES_* environment variables to be set from refget.agents import RefgetDBAgent agent = RefgetDBAgent() print(f"Connected to database via: {agent.engine}")

Connected to database via: Engine(postgresql://seqcol:***@localhost/seqcol)

Querying collections¶

With the demo setup, one sequence collection is pre-loaded. List the available collections:

In [2]:

# List available collections
collections = agent.seqcol.list_by_offset()
print(f"Available collections: {collections}")

# List available collections collections = agent.seqcol.list_by_offset() print(f"Available collections: {collections}")

Available collections: {'pagination': {'page': 0, 'page_size': 50, 'total': 1}, 'results': [SequenceCollection(digest='XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk', names_digest='Fw1r9eRxfOZD98KKrhlYQNEdSRHoVxAG', sorted_name_length_pairs_digest='zjM1Ie9m0zFbqsAnZ6jAJSXuFpKTr40J', sequences_digest='0uDQVLuHaOZi1u76LjV__yrVUIz9Bwhr', sorted_sequences_digest='KgWo6TT1Lqw6vgkXU9sYtCU9xwXoDt6M', lengths_digest='cGRMZIb3AVgkcAfNv39RN7hnT5Chk7RX', name_length_pairs_digest='B9MESWM8k-hK_OeQK8bZNAG74pLY0Ujq')]}

Retrieving a collection¶

Retrieve a specific collection by its digest:

In [3]:

# Retrieve a collection by digest
digest = "XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk"
collection = agent.seqcol.get(digest, return_format="level2")
print(f"Collection: {collection}")

# Retrieve a collection by digest digest = "XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk" collection = agent.seqcol.get(digest, return_format="level2") print(f"Collection: {collection}")

Collection: {'lengths': [8, 4, 4], 'names': ['chrX', 'chr1', 'chr2'], 'sequences': ['SQ.iYtREV555dUFKg2_agSJW6suquUyPpMw', 'SQ.YBbVX0dLKG1ieEDCiMmkrTZFt_Z5Vdaj', 'SQ.AcLxtBuKEPk_7PGE_H4dGElwZHCujwH6'], 'sorted_sequences': ['SQ.AcLxtBuKEPk_7PGE_H4dGElwZHCujwH6', 'SQ.YBbVX0dLKG1ieEDCiMmkrTZFt_Z5Vdaj', 'SQ.iYtREV555dUFKg2_agSJW6suquUyPpMw'], 'name_length_pairs': [{'length': 8, 'name': 'chrX'}, {'length': 4, 'name': 'chr1'}, {'length': 4, 'name': 'chr2'}]}

Comparing collections¶

Compare two sequence collections to identify their similarities and differences. In this demo, we'll compare a collection to itself (showing a perfect match):

In [4]:

# Compare a collection with itself (demonstrates the comparison feature)
digest = "XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk"
comparison = agent.compare_digests(digest, digest)
print(f"Comparison result: {comparison}")

# Compare a collection with itself (demonstrates the comparison feature) digest = "XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk" comparison = agent.compare_digests(digest, digest) print(f"Comparison result: {comparison}")

Comparison result: {'attributes': {'a_only': [], 'b_only': [], 'a_and_b': ['lengths', 'name_length_pairs', 'names', 'sequences', 'sorted_sequences']}, 'array_elements': {'a_count': {'lengths': 3, 'name_length_pairs': 3, 'names': 3, 'sequences': 3, 'sorted_sequences': 3}, 'b_count': {'lengths': 3, 'name_length_pairs': 3, 'names': 3, 'sequences': 3, 'sorted_sequences': 3}, 'a_and_b_count': {'lengths': 3, 'name_length_pairs': 3, 'names': 3, 'sequences': 3, 'sorted_sequences': 3}, 'a_and_b_same_order': {'lengths': True, 'name_length_pairs': True, 'names': True, 'sequences': True, 'sorted_sequences': True}}}

Sub-agents¶

The RefgetDBAgent provides access to specialized sub-agents:

Sub-agent	Purpose	Key Methods
agent.seqcol	Sequence collection operations	add_from_fasta_file(), get(), list_by_offset()
agent.seq	Individual sequence operations	get(), add(), list()
agent.fasta_drs	FASTA file DRS object management	get(), add(), add_access_method()
agent.pangenome	Pangenome operations	get(), add(), add_from_fasta_pep()
agent.attribute	Attribute array operations	get(), list(), search()

Summary

• RefgetDBAgent() connects to PostgreSQL using POSTGRES_* environment variables
• agent.seqcol.list_by_offset() and agent.seqcol.get(digest) for querying collections
• agent.compare_digests(a, b) compares two collections
• Sub-agents provide specialized operations: seqcol, seq, fasta_drs, pangenome, attribute