rotifer.db.ncbi.entrez.NucleotideFeaturesCursor#

class rotifer.db.ncbi.entrez.NucleotideFeaturesCursor(exclude_type=['source', 'gene', 'mRNA'], autopid=False, assembly=None, codontable='Bacterial', progress=True, tries=3, sleep_between_tries=1, batch_size=20, threads=10)[source]#

Bases: SequenceCursor

Fetch nucleotide annotation as feature tables.

Nucleotide entries are downloaded in GenBank format and converted to dataframes with one row per annotated feature.

Parameters:

exclude_typelist of str, default ['source', 'gene', 'mRNA']: Feature types to ignore.
autopidbool, default False: Automatically set protein identifiers.
assemblystr, optional: Assembly accession assigned to every parsed feature.
codontablestr or int, default ‘Bacterial’: Codon table used when the data does not define one.
progressbool, default True: Whether to print a progress bar.
triesint, default 3: Number of attempts to download data.
sleep_between_triesint, default 1: Number of seconds to wait between download attempts.
batch_sizeint, default 20: Number of accessions per batch.
threadsint, default 10: Number of simultaneous threads. Capped at 3 without an NCBI API key and at 10 with one.

Examples

>>> from rotifer.db.ncbi import entrez
>>> nfc = entrez.NucleotideFeaturesCursor()
>>> df = nfc.fetchall(['CP084314.1'])

fetchall(accessions)[source]#

Fetch the feature tables of all entries as one dataframe.

Parameters:

accessionslist of str: NCBI nucleotide accessions.

Returns:

pandas.DataFrame: The concatenated feature tables. Empty when nothing could be retrieved.

getids(obj)[source]#

Extract nucleotide accessions from feature tables.

Parameters:

objpandas.DataFrame or list of pandas.DataFrame: Feature tables produced by the cursor.

Returns:

set of str: The values of the nucleotide column.

parser(stream, accession)[source]#

Parse an EFetch GenBank stream into feature tables.

Parameters:

streamfile-like: Open stream returned by the fetcher.
accessionstr or iterable of str: The queried nucleotide accessions, kept for interface compatibility.

Returns:

list of pandas.DataFrame: One feature table per nucleotide sequence.