sugar._io.embl module

EMBL flat file reader for ENA and UniProt

EMBL stands for the European Molecular Biology Laboratory. ENA stands for the European Nucleotide Archive. UniProt stands for the Universal Protein Database.

sugar._io.embl.is_embl(f, **kw)

sugar._io.embl.is_fts_embl(f, **kw)

sugar._io.embl.iter_embl(f, exclude=(), genbank=True)

Read EMBL records and sequences from file into BioBasket

Parameters:

• exclude (tuple) – Tuple of feature names to exclude, possible options are 'seq', 'translation', 'fts' or line keys (e.g. 'CC').

• genbank – By default, use genbank like key names in the _embl meta data, if set to False will use EMBL two character keys, except for references which will be saved in the _embl.R attribute.

Warning

This function should NOT be called directly, it registers via read() and iter_(), call this instead.

sugar._io.embl.read_fts_embl(f, exclude=())

Read EMBL feature records from file into FeatureList

Parameters:

exclude (tuple) – Tuple of feature names to exclude, possible options are 'translation', 'fts', sequences are excluded anyway.

Warning

This function should NOT be called directly, it registers via read_fts(), call this instead.