rotifer.db.ncbi.ftp.GenomeFeaturesCursor#

class rotifer.db.ncbi.ftp.GenomeFeaturesCursor(exclude_type=['source', 'gene', 'mRNA'], autopid=False, codontable='Bacterial', progress=True, tries=3, batch_size=4, threads=15, timeout=10, cache='/tmp', *args, **kwargs)[source]#

Bases: GenomeFeaturesCursor, GenomeCursor

Fetch genome annotation from the NCBI FTP site as dataframes.

Genomes are downloaded like GenomeCursor does, then converted to feature tables 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.
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.
batch_sizeint, default 4: Number of accessions per batch.
threadsint, default 15: Number of processes used for parallel downloads.
timeoutint, default 10: Maximum time, in seconds, to wait for a server connection.
cachestr, optional: Directory for temporary files. Defaults to the rotifer cache directory.

Examples

Load the feature tables of two genomes:

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