Refget Python API Documentation

FASTA Processing

`fasta_to_seqcol_dict`

def fasta_to_seqcol_dict(fasta_file_path: Union[str, Path]) -> dict

Convert a FASTA file into a Sequence Collection dict.

Parameters:

fasta_file_path (Union[str, Path]): Path to the FASTA file

Returns:

dict: A canonical sequence collection dictionary

Raises:

ImportError: If gtars is not installed (required for FASTA processing)

`compare_seqcols`

def compare_seqcols(A: SeqColDict, B: SeqColDict) -> dict

Workhorse comparison function

Parameters:

A (SeqColDict): Sequence collection A
B (SeqColDict): Sequence collection B

Returns:

dict: Following formal seqcol specification comparison function return value

`calc_jaccard_similarities`

def calc_jaccard_similarities(A: SeqColDict, B: SeqColDict) -> dict[str, float]

Takes two sequence collections and calculates jaccard similarties for all attributes

Parameters:

A (SeqColDict): Sequence collection A
B (SeqColDict): Sequence collection B

Returns:

dict (dict[str, float]): Jaccard similarities for all attributes

`validate_seqcol`

def validate_seqcol(seqcol_obj: SeqColDict, schema=None) -> bool

Validate a seqcol object against the seqcol schema. Returns True if valid, raises InvalidSeqColError if not, which enumerates the errors. Retrieve individual errors with exception.errors

`validate_seqcol_bool`

def validate_seqcol_bool(seqcol_obj: SeqColDict, schema=None) -> bool

Validate a seqcol object against the seqcol schema. Returns True if valid, False if not.

To enumerate the errors, use validate_seqcol instead.

FastAPI Integration

`create_refget_router`

def create_refget_router(sequences: bool = False, collections: bool = True, pangenomes: bool = False, fasta_drs: bool = False, compliance: bool = True, refget_store_url: str = None, mount_prefix: str = '') -> APIRouter

Create a FastAPI router for the sequence collection API. This router provides endpoints for retrieving and comparing sequence collections. You can choose which endpoints to include by setting the sequences, collections, pangenomes, or fasta_drs flags.

Parameters:

sequences (bool): Include sequence endpoints (default: False)
collections (bool): Include sequence collection endpoints (default: True)
pangenomes (bool): Include pangenome endpoints (default: False)
fasta_drs (bool): Include FASTA DRS endpoints (default: False)
refget_store_url (str): URL of backing RefgetStore (e.g., s3://bucket/store/) (default: None)
mount_prefix (str): The path prefix this router will be included under, when it is included with include_router(..., prefix=...) rather than mounted as a sub-application. Only used so the compliance endpoints self-target the seqcol service instead of the server root. Leave empty when mounting an app (scope["root_path"] covers it). (default: '')

Returns:

APIRouter: A FastAPI router with the specified endpoints

Examples:

app.include_router(create_refget_router(fasta_drs=True), prefix="/seqcol")

Client Classes

The client module provides interfaces for interacting with refget-compliant servers.

`SequenceClient`

class SequenceClient(urls: list[str] = ['https://www.ebi.ac.uk/ena/cram'], raise_errors: Optional[bool] = None)

Bases: RefgetClient

A client for interacting with a refget sequences API.

Initializes the sequences client.

Parameters:

urls (list): A list of base URLs of the sequences API. Defaults to ["https://www.ebi.ac.uk/ena/cram/sequence/"]. (default: ['https://www.ebi.ac.uk/ena/cram'])
raise_errors (bool): Whether to raise errors or log them. Defaults to None, which will guess. (default: None)

Attributes: urls (list): The list of base URLs of the sequences API.

Attributes

raise_errors
urls

Methods

`get_metadata`

def get_metadata(digest: str) -> Optional[dict]

Retrieves metadata for a given sequence digest.

Parameters:

digest (str): The digest of the sequence.

Returns:

dict: The metadata.

`get_sequence`

def get_sequence(digest: str, start: Optional[int] = None, end: Optional[int] = None) -> Optional[str]

Retrieves a sequence for a given digest.

Parameters:

digest (str): The digest of the sequence.

Returns:

str: The sequence.

`SequenceCollectionClient`

class SequenceCollectionClient(urls: list[str] = ['https://seqcolapi.databio.org'], raise_errors: Optional[bool] = None)

Bases: RefgetClient

A client for interacting with a refget sequence collections API.

Initializes the sequence collection client.

Parameters:

urls (list): A list of base URLs of the sequence collection API. Defaults to ["https://seqcolapi.databio.org"]. (default: ['https://seqcolapi.databio.org'])

Attributes:

urls (list): The list of base URLs of the sequence collection API.

Attributes

raise_errors
urls

Methods

`aliases_for`

def aliases_for(digest: str, kind: str = 'collection') -> Optional[dict]

Reverse lookup: list all (namespace, alias) pairs for a digest.

Parameters:

digest (str): The digest to look up.
kind (str): "collection" (default) or "sequence". (default: 'collection')

Returns:

dict: {"digest": ..., "aliases": [[namespace, alias], ...]}.

`build_chrom_sizes`

def build_chrom_sizes(digest: str) -> str

Build a chrom.sizes file content for a sequence collection.

Format per line: NAME\tLENGTH

Parameters:

digest (str): The sequence collection digest

Returns:

str: String content of the chrom.sizes file

`build_fai`

def build_fai(digest: str) -> str

Build a complete .fai index file content for a FASTA.

FAI format per line: NAME\tLENGTH\tOFFSET\tLINEBASES\tLINEWIDTH

Parameters:

digest (str): The sequence collection digest

Returns:

str: String content of the .fai file

`compare`

def compare(digest1: str, digest2: str) -> Optional[dict]

Compares two sequence collections hosted on the server.

Parameters:

digest1 (str): The digest of the first sequence collection.
digest2 (str): The digest of the second sequence collection.

Returns:

dict: The JSON response containing the comparison of the two sequence collections.

`compare_local`

def compare_local(digest: str, local_collection: dict) -> Optional[dict]

Compares a server-hosted sequence collection with a local collection.

Parameters:

digest (str): The digest of the server-hosted sequence collection.
local_collection (dict): A level 2 sequence collection representation.

Returns:

dict: The JSON response containing the comparison.

`download_fasta`

def download_fasta(digest: str, dest_path: str = None, access_id: str = None) -> str

Download the FASTA file to a local path.

Parameters:

digest (str): The sequence collection digest
dest_path (str): Destination file path. If None, uses object name. (default: None)
access_id (str): Specific access method to use. If None, tries all. (default: None)

Returns:

str: Path to downloaded file

Raises:

ValueError: If no access methods available or specified access_id not found

`download_fasta_to_store`

def download_fasta_to_store(digest: str, store: 'RefgetStore', access_id: str = None, temp_dir: str = None, namespaces: Optional[list[str]] = None) -> str

Download the FASTA file and import it into a RefgetStore.

This method downloads the FASTA file from the DRS endpoint and immediately imports it into the provided RefgetStore, enabling local sequence retrieval by digest without re-downloading.

Parameters:

digest (str): The sequence collection digest
store (RefgetStore): The RefgetStore instance to import into
access_id (str): Specific access method to use. If None, tries all. (default: None)
temp_dir (str): Directory for temporary download. If None, uses system temp. (default: None)

Returns:

str: The collection digest of the imported sequences

Raises:

ValueError: If no access methods available or specified access_id not found
ImportError: If gtars/RefgetStore is not available

>>> from refget.store import RefgetStore
>>> from refget.clients import SequenceCollectionClient
>>> store = RefgetStore.in_memory()
>>> client = SequenceCollectionClient()
>>> collection_digest = client.download_fasta_to_store("abc123", store)
>>> # Now you can retrieve sequences by digest from the local store
>>> seq = store.get_substring(sequence_digest, 0, 100)

`get_attribute`

def get_attribute(attribute: str, digest: str) -> Optional[dict]

Retrieves a specific attribute value by its digest.

Parameters:

attribute (str): The attribute name (e.g., "names", "lengths", "sequences").
digest (str): The level 1 digest of the attribute.

Returns:

dict: The JSON response containing the attribute value.

`get_collection`

def get_collection(digest: str, level: int = 2) -> Optional[dict]

Retrieves a sequence collection for a given digest and detail level.

Parameters:

digest (str): The digest of the sequence collection.
level (int): The level of detail for the sequence collection. Defaults to 2. (default: 2)

Returns:

dict: The JSON response containing the sequence collection.

`get_fasta`

def get_fasta(digest: str) -> Optional[dict]

Get DRS object metadata for a FASTA file.

Parameters:

digest (str): The sequence collection digest (which is also the DRS object ID)

Returns:

dict: DRS object with id, self_uri, size, checksums, access_methods, etc.

`get_fasta_index`

def get_fasta_index(digest: str) -> Optional[dict]

Get FAI index data for a FASTA file.

Parameters:

digest (str): The sequence collection digest

Returns:

dict: Dict with line_bases, extra_line_bytes, offsets

`get_fhr`

def get_fhr(digest: str) -> Optional[dict]

Get FHR metadata for a collection.

Parameters:

digest (str): The collection digest.

Returns:

dict: FHR metadata, or None if not found.

`get_refget_store`

def get_refget_store(cache_dir: str) -> 'RefgetStore'

Get a RefgetStore instance connected to the server's backing store.

Parameters:

cache_dir (str): Local directory for caching store data

Returns:

RefgetStore: RefgetStore instance loaded from remote

Raises:

ValueError: If server doesn't have a RefgetStore configured
ImportError: If gtars is not installed

`get_refget_store_url`

def get_refget_store_url() -> Optional[str]

Discover RefgetStore URL from service-info if available.

Returns:

str: The RefgetStore URL if configured, None otherwise.

`get_regions`

def get_regions(digest: str, regions: list) -> Optional[list]

Extract region substrings from a server-hosted sequence collection.

Posts a list of regions to the server's region-extraction endpoint and returns the structured results. Requires a store-backed server (the database backend responds with HTTP 501).

Parameters:

digest (str): The collection digest to extract regions from.
regions (list): A list of {"chrom", "start", "end"} dicts.

Returns:

list: A list of {"chrom_name", "start", "end", "sequence"} dicts.

`is_aliases_enabled`

def is_aliases_enabled() -> bool

Check if alias endpoints are advertised in service-info.

Returns:

bool: True if aliases are enabled, False otherwise.

`is_fasta_drs_enabled`

def is_fasta_drs_enabled() -> bool

Check if FastaDRS endpoints are available.

Returns:

bool: True if FastaDRS is enabled, False otherwise.

`is_fhr_enabled`

def is_fhr_enabled() -> bool

Check if FHR metadata is advertised in service-info.

Returns:

bool: True if FHR metadata is enabled, False otherwise.

`list_alias_namespaces`

def list_alias_namespaces(kind: str = 'collection') -> Optional[dict]

List alias namespaces for the given kind.

Parameters:

kind (str): "collection" (default) or "sequence". (default: 'collection')

Returns:

dict: {"namespaces": [...]}.

`list_aliases`

def list_aliases(namespace: str, kind: str = 'collection') -> Optional[dict]

List aliases within a namespace.

Parameters:

namespace (str): The alias namespace.
kind (str): "collection" (default) or "sequence". (default: 'collection')

Returns:

dict: {"namespace": ..., "aliases": [...]}.

`list_attributes`

def list_attributes(attribute: str, page: Optional[int] = None, page_size: Optional[int] = None) -> Optional[dict]

Lists all available values for a given attribute with optional paging support.

Parameters:

attribute (str): The attribute to list values for.
page (int): The page number to retrieve. Defaults to None. (default: None)
page_size (int): The number of items per page. Defaults to None. (default: None)

Returns:

dict: The JSON response containing the list of available values for the attribute.

`list_collections`

def list_collections(page: Optional[int] = None, page_size: Optional[int] = None, **filters) -> Optional[dict]

Lists all available sequence collections with optional paging and attribute filtering support.

Parameters:

page (int): The page number to retrieve. Defaults to None. (default: None)
page_size (int): The number of items per page. Defaults to None. (default: None)
**filters (Any): Optional attribute filters (e.g., names="abc123", lengths="def456"). Values should be level 1 digests of the attributes. (default: {})

Returns:

dict: The JSON response containing the list of available sequence collections.

`list_fhr`

def list_fhr() -> Optional[dict]

List collections that have FHR metadata.

Returns:

dict: {"collections": [...]}.

`resolve_alias`

def resolve_alias(namespace: str, alias: str, kind: str = 'collection') -> Optional[dict]

Resolve a namespace:alias to a digest.

Parameters:

namespace (str): The alias namespace.
alias (str): The alias name.
kind (str): "collection" (default) or "sequence". (default: 'collection')

Returns:

dict: {"namespace": ..., "alias": ..., "digest": ...} or None.

`service_info`

def service_info() -> Optional[dict]

Retrieves information about the service.

Returns:

dict: The service information.

`write_chrom_sizes`

def write_chrom_sizes(digest: str, dest_path: str) -> str

Write a chrom.sizes file for a sequence collection.

Parameters:

digest (str): The sequence collection digest
dest_path (str): Path to write the chrom.sizes file

Returns:

str: Path to the written file

`write_fai`

def write_fai(digest: str, dest_path: str) -> str

Write a .fai index file for a FASTA.

Parameters:

digest (str): The sequence collection digest
dest_path (str): Path to write the .fai file

Returns:

str: Path to the written file

`FastaDrsClient`

class FastaDrsClient(urls: list[str] = ['https://seqcolapi.databio.org/fasta'], raise_errors: Optional[bool] = None)

Bases: RefgetClient

A client for interacting with FASTA files via GA4GH DRS endpoints.

Initializes the FASTA DRS client.

Parameters:

urls (list): A list of base URLs of the FASTA DRS API. Defaults to ["https://seqcolapi.databio.org/fasta"]. (default: ['https://seqcolapi.databio.org/fasta'])
raise_errors (bool): Whether to raise errors or log them. Defaults to None, which will guess. (default: None)

Attributes:

urls (list): The list of base URLs of the FASTA DRS API.

Attributes

raise_errors
urls

Methods

`build_fai`

def build_fai(digest: str, seqcol_client: 'SequenceCollectionClient' = None) -> str

Build a complete .fai index file content for a FASTA.

FAI format per line: NAME LENGTH OFFSET LINEBASES LINEWIDTH

Parameters:

digest (str): The sequence collection digest
seqcol_client (SequenceCollectionClient): SequenceCollectionClient to use. If None, uses parent client or creates one. (default: None)

Returns:

str: String content of the .fai file

`download`

def download(digest: str, dest_path: str = None, access_id: str = None) -> str

Download the FASTA file to a local path.

Parameters:

digest (str): The sequence collection digest
dest_path (str): Destination file path. If None, uses object name. (default: None)
access_id (str): Specific access method to use. If None, tries all. (default: None)

Returns:

str: Path to downloaded file

Raises:

ValueError: If no access methods available or specified access_id not found

`download_to_store`

def download_to_store(digest: str, store: 'RefgetStore', access_id: str = None, temp_dir: str = None, namespaces: Optional[list[str]] = None) -> str

Download the FASTA file and import it into a RefgetStore.

This method downloads the FASTA file from the DRS endpoint and immediately imports it into the provided RefgetStore, enabling local sequence retrieval by digest without re-downloading.

Parameters:

digest (str): The sequence collection digest
store (RefgetStore): The RefgetStore instance to import into
access_id (str): Specific access method to use. If None, tries all. (default: None)
temp_dir (str): Directory for temporary download. If None, uses system temp. (default: None)
namespaces (list[str]): Namespace prefixes to extract aliases from FASTA headers when importing into the store. (default: None)

Returns:

str: The collection digest of the imported sequences

Raises:

ValueError: If no access methods available or specified access_id not found
ImportError: If gtars/RefgetStore is not available

`get_access_url`

def get_access_url(digest: str, access_id: str) -> Optional[dict]

Get access URL for a specific access method.

Parameters:

digest (str): The sequence collection digest
access_id (str): The access ID from the access method

Returns:

dict: Access URL object

`get_index`

def get_index(digest: str) -> Optional[dict]

Get FAI index data for a FASTA file.

Parameters:

digest (str): The sequence collection digest

Returns:

dict: Dict with line_bases, extra_line_bytes, offsets

`get_object`

def get_object(digest: str) -> Optional[dict]

Get DRS object metadata for a FASTA file.

Parameters:

digest (str): The sequence collection digest (which is also the DRS object ID)

Returns:

dict: DRS object with id, self_uri, size, checksums, access_methods, etc.

`service_info`

def service_info() -> Optional[dict]

Get DRS service info.

Returns:

dict: The service information.

`write_fai`

def write_fai(digest: str, dest_path: str, seqcol_client: 'SequenceCollectionClient' = None) -> str

Write a .fai index file for a FASTA.

Parameters:

digest (str): The sequence collection digest
dest_path (str): Path to write the .fai file
seqcol_client (SequenceCollectionClient): SequenceCollectionClient to use (default: None)

Returns:

str: Path to the written file

`PangenomeClient`

class PangenomeClient

Bases: RefgetClient

Agent Classes

Agents provide higher-level abstractions for working with refget data in a PostgreSQL database.

`RefgetDBAgent`

class RefgetDBAgent(engine: Optional[SqlalchemyDatabaseEngine] = None, postgres_str: Optional[str] = None, schema=SEQCOL_SCHEMA_PATH, inherent_attrs: List[str] = DEFAULT_INHERENT_ATTRS, fasta_drs_url_prefix: Optional[str] = None)

Primary aggregator agent, interface to all other agents

Parameterized it via these environment variables:

POSTGRES_HOST
POSTGRES_DB
POSTGRES_USER
POSTGRES_PASSWORD

Attributes

engine
inherent_attrs
schema_dict

Properties

`attribute`

@property
def attribute -> AttributeAgent

`fasta_drs`

@property
def fasta_drs -> FastaDrsAgent

`pangenome`

@property
def pangenome -> PangenomeAgent

`seq`

@property
def seq -> SequenceAgent

`seqcol`

@property
def seqcol -> SequenceCollectionAgent

Methods

`aliases_for`

def aliases_for(kind: str, digest: str) -> list

`calc_similarities`

def calc_similarities(digestA: str, digestB: str) -> dict

Calculates the Jaccard similarity between two sequence collections.

This method retrieves two sequence collections using their digests and then computes jaccard similarities for all attributes.

Parameters:

digestA (str): The digest (identifier) for the first sequence collection.
digestB (str): The digest (identifier) for the second sequence collection.

Returns:

dict: The Jaccard similarity score between the two sequence collections for all present and shared attributes.

`calc_similarities_seqcol_dicts`

def calc_similarities_seqcol_dicts(seqcolA: dict, seqcolB: dict) -> dict

Calculates the Jaccard similarity between two sequence collections.

This method retrieves one sequence collections using a digests and then computes jaccard similarities versus another input sequence collection dictionary.

Parameters:

seqcolA (dict): the first sequence collection in dict format.
seqcolB (dict): the second sequence collection in dict format.

Returns:

dict: The Jaccard similarity score between the two sequence collections for all present and shared attributes.

`capabilities`

def capabilities() -> dict

`collection_count`

def collection_count() -> int

`compare_1_digest`

def compare_1_digest(digestA: str, seqcolB: dict) -> dict

`compare_digest_with_level2`

def compare_digest_with_level2(digest: str, level2_b: dict) -> dict

`compare_digests`

def compare_digests(digestA: str, digestB: str) -> dict

`get_attribute`

def get_attribute(attribute_name: str, attribute_digest: str) -> list

`get_collection`

def get_collection(digest: str, level: int = 2) -> dict

`get_collection_attribute`

def get_collection_attribute(digest: str, attribute: str) -> list

`get_collection_itemwise`

def get_collection_itemwise(digest: str, limit: int | None = None) -> list[dict]

`get_fhr`

def get_fhr(digest: str)

`list_alias_namespaces`

def list_alias_namespaces(kind: str) -> list

`list_aliases`

def list_aliases(kind: str, namespace: str) -> list

`list_attributes`

def list_attributes(attribute: str, page: int = 0, page_size: int = 100) -> dict

`list_collections`

def list_collections(page: int = 0, page_size: int = 100, filters: dict | None = None) -> dict

`list_fhr`

def list_fhr() -> list

`resolve_alias`

def resolve_alias(kind: str, namespace: str, alias: str)

`retrieve_level2_digest`

def retrieve_level2_digest(seqcoldigest: str) -> dict

`truncate`

def truncate() -> int

Delete all records from the database

`SequenceCollectionAgent`

class SequenceCollectionAgent(engine: SqlalchemyDatabaseEngine, inherent_attrs: Optional[List[str]] = None, parent: Optional['RefgetDBAgent'] = None)

Agent for interacting with database of sequence collection

Attributes

engine
inherent_attrs
parent

Methods

`add`

def add(seqcol: SequenceCollection, update: bool = False) -> SequenceCollection

Add a sequence collection to the database or update it if it exists

Parameters:

seqcol (SequenceCollection): The sequence collection to add
update (bool): If True, update an existing collection if it exists (default: False)

Returns:

SequenceCollection: The added or updated sequence collection

`add_from_dict`

def add_from_dict(seqcol_dict: dict, update: bool = False) -> SequenceCollection

Add a sequence collection from a seqcol dictionary

Parameters:

seqcol_dict (dict): The sequence collection in dictionary form
update (bool): If True, update an existing collection if it exists (default: False)

Returns:

SequenceCollection: The added or updated sequence collection

`add_from_fasta_file`

def add_from_fasta_file(fasta_file_path: str, update: bool = False, create_fasta_drs: bool = True, human_readable_name: str = None) -> SequenceCollection

Given a path to a fasta file, load the sequences into the refget database.

Parameters:

fasta_file_path (str): Path to the fasta file
update (bool): If True, update an existing collection if it exists (default: False)
create_fasta_drs (bool): If True, create a FastaDrsObject for the FASTA file (default: True)
human_readable_name (str): Optional human-readable name for the collection (default: None)

Returns:

SequenceCollection: The added or updated sequence collection

`add_from_fasta_file_with_name`

def add_from_fasta_file_with_name(fasta_file_path: str, human_readable_name: str, update: bool = False, create_fasta_drs: bool = True) -> SequenceCollection

Given a path to a fasta file, and a human-readable name, load the sequences into the refget database.

Deprecated: Use add_from_fasta_file(fasta_file_path, human_readable_name=name) instead.

`add_from_fasta_pep`

def add_from_fasta_pep(pep: 'peppy.Project', fa_root: str, update: bool = False, create_fasta_drs: bool = True) -> dict

Given a PEP project and a root directory containing the fasta files, load the fasta files into the refget database.

Parameters:

pep (peppy.Project): PEP project object containing sample metadata
fa_root (str): Root directory containing the fasta files
update (bool): If True, update existing sequence collections (default: False)
create_fasta_drs (bool): If True, create FastaDrsObjects for the FASTA files (default: True)

Returns:

dict: A dictionary of the digests of the added sequence collections

`get`

def get(digest: str, return_format: str = 'level2', attribute: Optional[str] = None, itemwise_limit: Optional[int] = None) -> SequenceCollection | dict | list

Get a sequence collection by digest

Parameters:

digest (str): The digest of the sequence collection
return_format (str): The format in which to return the sequence collection (default: 'level2')
attribute (str): Name of an attribute to return, if you just want an attribute (default: None)
itemwise_limit (int): Limit the number of items returned in itemwise format (default: None)

Returns:

SequenceCollection: The sequence collection (in requested format)

`get_many_level2_offset`

def get_many_level2_offset(limit: int = 50, offset: int = 0, target_digests: Optional[List[str]] = None) -> ResultsSequenceCollections

`list`

def list(page_size: int = 100, cursor: Optional[str] = None) -> dict

`list_by_offset`

def list_by_offset(limit: int = 50, offset: int = 0) -> dict

`search_by_attributes`

def search_by_attributes(filters: dict, offset: int = 0, limit: int = 50) -> dict

Search sequence collections by multiple attribute filters (AND logic).

Parameters:

filters (dict): Dict of {attribute_name: digest} pairs
offset (int): Pagination offset (default: 0)
limit (int): Max results to return (default: 50)

Returns:

dict: Dict with pagination info and results

`SequenceAgent`

class SequenceAgent(engine: SqlalchemyDatabaseEngine)

Agent for interacting with database of sequences

Attributes

engine

Methods

`add`

def add(sequence: Sequence) -> Sequence

`get`

def get(digest: str, start: int | None = None, end: int | None = None) -> str

`list`

def list(offset: int = 0, limit: int = 50) -> dict

`PangenomeAgent`

class PangenomeAgent(parent: 'RefgetDBAgent')

Agent for interacting with database of pangenomes

Attributes

engine
parent

Methods

`add`

def add(pangenome: Pangenome) -> Pangenome

`add_from_fasta_pep`

def add_from_fasta_pep(pep: 'peppy.Project', fa_root: str, update: bool = False) -> Pangenome

`get`

def get(digest: str, return_format: str = 'level2') -> Pangenome | dict

`list_by_offset`

def list_by_offset(limit: int = 50, offset: int = 0) -> dict

`AttributeAgent`

class AttributeAgent(engine: SqlalchemyDatabaseEngine)

Attributes

engine

Methods

`get`

def get(attribute_type: str, digest: str) -> list

`list`

def list(attribute_type: str, offset: int = 0, limit: int = 50) -> dict

`search`

def search(attribute_type: str, digest: str, offset: int = 0, limit: int = 50) -> dict

`FastaDrsAgent`

class FastaDrsAgent(engine: SqlalchemyDatabaseEngine, url_prefix: Optional[str] = None)

Agent for interacting with database of FASTA DRS objects

Attributes

engine
url_prefix

Methods

`add`

def add(fasta_drs: FastaDrsObject) -> FastaDrsObject

Add a FastaDrsObject to the database

`add_access_method`

def add_access_method(digest: str, access_method: AccessMethod) -> FastaDrsObject

Add an access method to an existing FastaDrsObject.

Parameters:

digest (str): The digest (object_id) of the DRS object
access_method (AccessMethod): The AccessMethod to add

Returns:

FastaDrsObject: The updated FastaDrsObject

`get`

def get(digest: str) -> FastaDrsObject

Get a FastaDrsObject by its digest (object_id)

`list_by_offset`

def list_by_offset(limit: int = 50, offset: int = 0) -> dict

List FastaDrsObjects with pagination

RefgetStore (gtars)

RefgetStore provides high-performance local sequence storage implemented in Rust. It supports:

In-memory and on-disk storage with optional compression
Remote store access with local caching
Sequence retrieval by digest or by collection + name
BED file region extraction for batch operations
FASTA export for individual sequences or regions

See the RefgetStore tutorial for usage examples.

RefgetStore, digest_fasta, compute_fai, digest_sequence, SequenceCollection, StorageMode, and sha512t24u_digest are implemented in Rust in gtars and re-exported by refget. Their API reference is in the gtars docs: gtars refget API reference.

Digest Functions

Low-level functions for computing GA4GH digests:

`canonical_str`

def canonical_str(item: dict) -> bytes

Convert a dict into a canonical string representation