rotifer.db.ncbi.entrez.GeneNeighborhoodCursor#

class rotifer.db.ncbi.entrez.GeneNeighborhoodCursor(column='pid', before=7, after=7, min_block_distance=0, strand=None, fttype='same', eukaryotes=False, exclude_type=['source', 'gene', 'mRNA'], autopid=False, codontable='Bacterial', progress=True, tries=3, sleep_between_tries=1, batch_size=20, threads=10)[source]#

Bases: GeneNeighborhoodCursor, NucleotideFeaturesCursor

Fetch gene neighborhoods from nucleotide annotation.

Target proteins are first resolved to nucleotide sequences through identical protein group (IPG) reports, and the annotated regions around each target are then extracted from the nucleotide entries downloaded with EFetch. This backend does not require a genome assembly, so it also covers proteins encoded on unassembled sequences.

Parameters:

columnstr, default ‘pid’

Name of the column to scan for matches to the accessions. See rotifer.genome.data.NeighborhoodDF.

beforeint, default 7

Keep at most this number of features, of the same type as the target, before each target.

afterint, default 7

Keep at most this number of features, of the same type as the target, after each target.

min_block_distanceint, default 0

Minimum distance between two consecutive blocks.

strandstr, optional

How to evaluate rows concerning the value of the strand column. Supported values:

None : ignore strand
same : same strand as the targets
+ : positive strand features and targets only
- : negative strand features and targets only

fttype{‘same’, ‘any’}, default ‘same’

How to process feature types of neighbors. With same, only features of the same type as the target are considered. With any, all features count when setting neighborhood boundaries.

eukaryotesbool, default False

Whether to process eukaryotic nucleotide sequences.

exclude_typelist of str, default ['source', 'gene', 'mRNA']

Feature types to ignore.

autopidbool, default False

Automatically set protein identifiers.

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.

See also

rotifer.db.ncbi.GeneNeighborhoodCursor: delegator that combines this backend with the FTP and mirror backends

Examples

>>> from rotifer.db.ncbi import entrez
>>> gnc = entrez.GeneNeighborhoodCursor(progress=True)
>>> df = gnc.fetchall(["EEE9598493.1"])

__getitem__(accessions, ipgs=None)[source]#

Find gene neighborhoods around one or more target proteins.

Parameters:

accessionsstr or iterable of str: NCBI protein accessions.
ipgspandas.DataFrame, optional: Precomputed identical protein group reports. When not given, they are downloaded with IPGCursor.

Returns:

rotifer.genome.data.NeighborhoodDF: The neighborhoods found. Empty when nothing could be retrieved.

fetchone(accessions, ipgs=None)[source]#

Iterate over gene neighborhoods as downloads complete.

Results are yielded in completion order, not input order.

Parameters:

accessionslist of str: NCBI protein identifiers.
ipgspandas.DataFrame, optional: Precomputed identical protein group reports, used to avoid downloading IPGs again.

Yields:

rotifer.genome.data.NeighborhoodDF: One dataframe per retrieved gene neighborhood.

getids2(obj, *args, **kwargs)[source]#

List protein identifiers per nucleotide sequence.

Parameters:

objpandas.DataFrame: A neighborhood dataframe.

Returns:

list of str: The identifiers found in the pid and, when present, replaced columns.

nucleotide_ids(obj)[source]#

Extract nucleotide accessions from neighborhood dataframes.

Parameters:

objpandas.DataFrame or list of pandas.DataFrame: Neighborhood dataframes.

Returns:

set of str: The unique values of the nucleotide column.

parser(stream, accession, proteins)[source]#

Extract gene neighborhoods from a nucleotide stream.

Parameters:

streamfile-like: Open stream returned by the fetcher.
accessionstr: Nucleotide accession.
proteinsdict: Mapping of each target protein accession to its identical protein group representative.

Returns:

list of rotifer.genome.data.NeighborhoodDF: The neighborhoods found, one dataframe per nucleotide sequence, each with a replaced column mapping proteins to the queries they represent.

Raises:

ValueError: If the sequence is eukaryotic and eukaryotes is False.

splitter(accessions, ipgs)[source]#

Group targets and their IPG rows into per-nucleotide batches.

Parameters:

accessionsset of str: Target protein accessions.
ipgspandas.DataFrame: Identical protein group reports restricted to the selected nucleotide sequences.

Returns:

list of list of tuple: Batches of (proteins, ipg_rows) pairs, one pair per nucleotide sequence, at most batch_size pairs per batch.

worker(chunk)[source]#

Process one batch of nucleotide sequences in a worker process.

Parameters:

chunklist of tuple: Batch entries produced by splitter(). Each entry holds a set of target protein accessions and the IPG rows of one nucleotide sequence.

Returns:

dict: A dictionary with two keys: result, a list of neighborhood dataframes (one per gene block), and missing, the registry of entries that could not be retrieved.