rotifer.db.ncbi.entrez.FastaCursor#

class rotifer.db.ncbi.entrez.FastaCursor(database='protein', progress=True, tries=3, sleep_between_tries=1, batch_size=20, threads=10, *args, **kwargs)[source]#

Bases: SequenceCursor

Fetch sequences from NCBI as FASTA, without annotations.

Identical to SequenceCursor except that data is downloaded in FASTA format, which is faster but carries no annotation.

Parameters:

databasestr, default ‘protein’: A valid NCBI sequence database name.
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
>>> fc = entrez.FastaCursor()
>>> seqs = fc.fetchall(["YP_009724395.1"])