rotifer.db.ncbi.mirror.GenomeFeaturesCursor#

class rotifer.db.ncbi.mirror.GenomeFeaturesCursor(path='/databases/genomes', exclude_type=['source', 'gene', 'mRNA'], autopid=False, codontable='Bacterial', progress=False, tries=1, batch_size=None, threads=2, *args, **kwargs)[source]#

Bases: GenomeFeaturesCursor, GenomeCursor

Fetch genome annotation from a local mirror as dataframes.

Genomes are read like GenomeCursor does, then converted to feature tables with one row per annotated feature.

Parameters:

pathstr, optional: Path to a mirror of the genomes section of the NCBI FTP site.
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 False: Whether to print a progress bar.
triesint, default 1: Accepted for interface compatibility; local reads are attempted only once.
batch_sizeint, optional: Number of accessions per batch.
threadsint, optional: Number of processes used for parallel reads.

Examples

Load the feature tables of two genomes:

>>> from rotifer.db.ncbi import mirror
>>> g = ['GCA_018744545.1', 'GCA_901308185.1']
>>> gfc = mirror.GenomeFeaturesCursor()
>>> df = gfc.fetchall(g)