cas.accession package

Submodules

cas.accession.base_accession_manager module

class cas.accession.base_accession_manager.BaseAccessionManager[source]

Bases: object

Abstract Accession ID generator.

abstract generate_accession_id(id_recommendation=None, labelset=None, cellset_name=None)[source]
Return type:

str

Parameters:

  • id_recommendation (str | None)

  • labelset (str | None)

  • cellset_name (str | None)

Generates an auto-increment based accession id. If the recommended accession_id is available, uses it. Params:

id_recommendation: accession id recommendation. Function uses this id if it is available, provides an auto-incremented id otherwise. labelset: Labelset name. If provided, uses it as a prefix to the accession id. cellset_name: Name of the cell set for which the accession ID is being generated.

Return: accession_id

cas.accession.hash_accession_manager module

class cas.accession.hash_accession_manager.HashAccessionManager(accession_prefix=None, digest_size=5)[source]

Bases: BaseAccessionManager

generate_accession_id(id_recommendation=None, cell_ids=None, labelset=None, suppress_warnings=False, cellset_name=None)[source]
Return type:

str

Parameters:

  • id_recommendation (str | None)

  • cell_ids (List | None)

  • labelset (str | None)

  • cellset_name (str | None)

Generates a Blake2b hashing algorithm based hash for the given cell IDs. Params:

id_recommendation: pre-calculated hash accession recommendation. Returns this value if recommendation is a valid accession id. cell_ids: Cell IDs list. Algorithm sorts cell ids internally. labelset: Labelset name. If provided, uses it as a prefix to the accession id. suppress_warnings: If True, suppresses warnings. cellset_name: this parameter is not utilized in this implementation.

Return: accession_id

cas.accession.hash_accession_manager.is_hash_accession(accession_id)[source]

Checks if the given accession is a valid hash accession. Hash accessions are 10 char long and only has hexdigits :type accession_id: str :param accession_id: accession to check

Returns: True if value is a valid hash accession id, false otherwise.

Parameters:

accession_id (str)

cas.accession.incremental_accession_manager module

class cas.accession.incremental_accession_manager.IncrementalAccessionManager(accession_prefix=None, last_accession_id=0)[source]

Bases: BaseAccessionManager

Numerically incremental Accession ID generator.

generate_accession_id(id_recommendation=None, labelset=None, cellset_name=None)[source]
Return type:

str

Parameters:

  • id_recommendation (str | None)

  • labelset (str | None)

  • cellset_name (str | None)

Generates an auto-increment based accession id. If the recommended accession_id is available, uses it. Params:

id_recommendation: accession id recommendation. Function uses this id if it is available, provides an auto-incremented id otherwise. labelset: this parameter is not utilized in this implementation. cellset_name: this parameter is not utilized in this implementation.

Return: accession_id

Module contents