rotifer.db.local.easel.FastaCursor

class rotifer.db.local.easel.FastaCursor(database_path=['/databases/fadb/nr/nr'], progress=True, tries=1, batch_size=200, threads=2, *args, **kwargs)

Bases: SimpleParallelProcessCursor

Fetch biomolecular sequences with Easel’s esl-sfetch.

Each database file is checked at construction time: files that do not exist are dropped and missing .ssi indices are built by running esl-sfetch --index.

Parameters:

database_pathstr or list of str, optional

Paths to FASTA files. Defaults to the local_database_path configuration entry.

progressbool, default True

Whether to print a progress bar.

triesint, default 1

Accepted for interface compatibility; local reads are attempted only once.

batch_sizeint, default 200

Number of accessions per batch.

threadsint, optional

Number of simultaneous processes. Defaults to half of the CPU count.

See also

rotifer.db.ncbi.FastaCursor

delegator that falls back to NCBI

Examples

>>> from rotifer.db.local import easel
>>> fc = easel.FastaCursor("/databases/fadb/nr/nr")
>>> seqs = fc.fetchall(["WP_063732599.1"])

fetcher(accession, *args, **kwargs)

Run esl-sfetch and collect its FASTA output.

Each configured database file is searched in turn until every accession is found or every file was tried. Accessions not found in any database are registered as missing.

Parameters:

accessionstr or iterable of str

Sequence accessions.

Returns:

io.StringIO

The concatenated FASTA output.

getids(obj)

Extract accessions from sequence records.

Parameters:

objBio.SeqRecord.SeqRecord or list of Bio.SeqRecord.SeqRecord

Sequence records produced by the cursor.

Returns:

set of str

The record identifiers.

parser(stream, accession, *args, **kwargs)

Parse a FASTA stream into sequence records.

NCBI style concatenated descriptions are trimmed to the first entry.

Parameters:

streamfile-like

Stream returned by fetcher().

accessionstr or iterable of str

Sequence accessions, kept for interface compatibility.

Returns:

list of Bio.SeqRecord.SeqRecord

The parsed records.