rotifer.db.sql.sqlite3.IPGCursor#

class rotifer.db.sql.sqlite3.IPGCursor(path, replace=False, identical='c100', identical_column='c100i100', *args, **kwargs)[source]#

Fetch identical protein group (IPG) reports from a local SQLite3 database.

Depending on identical, results are built either from a precomputed non-redundant clustering table (nr) or directly from the features table.

Parameters:

pathstr: Path to a local SQLite3 database.
replacebool, default False: If True, overwrite the database file.
identicalstr or None, default ‘c100’: Name of the clustering column used to group identical proteins. If None, IPGs are derived from features alone.
identical_columnstr, default ‘c100i100’: Column added to the report identifying the cluster representative.

See also

Examples

>>> from rotifer.db.sql import sqlite3 as rdss
>>> ic = rdss.IPGCursor("genomes.sqlite3")
>>> df = ic.fetchall("YP_009724395.1")

__getitem__(accessions)[source]#

Fetch identical protein group reports, dictionary style.

Parameters:

Returns:

pandas.DataFrame: Columns as listed in self._columns plus self._added_columns. Empty if the SQL file for the selected identical mode could not be found.

fetchall(accessions)[source]#

Fetch identical protein group reports for all accessions at once.

Parameters:

Returns: