rotifer.db.delegator.SequentialDelegatorCursor

class rotifer.db.delegator.SequentialDelegatorCursor(readers=[], writers=[], progress=True, tries=None, batch_size=None, threads=None, *args, **kwargs)

Bases: DelegatorCursor

Delegator that queries its backends one after the other.

Backends listed in readers are tried in order and each one only receives the identifiers that previous backends could not resolve. Results retrieved by a reader are handed to every backend listed in writers for storage.

Parameters:

readerslist of str, default []

Names of the backend modules used to retrieve data, in order of preference.

writerslist of str, default []

Names of the backend modules used to store retrieved data.

progressbool, default True

Whether to print a progress bar.

triesint, optional

Number of attempts to download each batch.

batch_sizeint, optional

Number of accessions per batch.

threadsint, optional

Number of simultaneous threads.

See also

rotifer.db.ncbi.SequenceCursor

a concrete sequential delegator

__getitem__(accessions, *args, **kwargs)

Fetch data for one or more entries, dictionary style.

Parameters:

accessionsstr or list of str

Database identifiers.

Returns:

object

The value returned by the delegated cursors: a single result object when a single accession yields a single result, otherwise a list of result objects.

Examples

>>> import rotifer.db.ncbi as ncbi
>>> tc = ncbi.TaxonomyCursor(progress=False)
>>> t = tc[2599]

fetchall(accessions, *args, **kwargs)

Fetch data for all accessions.

Parameters:

accessions: list of database identifiers

Database identifiers.

Returns:

Pandas dataframe

fetchone(accessions, *args, **kwargs)

Get a generator to fetch data for iteratively.

Parameters:

accessions: list of strings

Database identifiers.

Returns:

Generator of Pandas dataframes