sugar._io.tab.core module

Generic tabular feature reader that is used by several plugins

sugar._io.tab.core.extract_seqs(fts, x='source', change_id=False)

Extract sequences from BLAST features and return BioBasket

Parameters:

x – One of 'source' or 'query'

sugar._io.tab.core.get_query_fts(fts)

Convert BLAST source features to query features

sugar._io.tab.core.read_tabular(f, *, sep='\t', outfmt=None, ftype=None, fmt='blast', comments=None)

Reader function used by BLAST, Infernal and MMseqs2 readers