Bio.SearchIO.ExonerateIO.exonerate_text module

Bio.SearchIO parser for Exonerate plain text output format.

class Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser(handle)

Bases: Bio.SearchIO.ExonerateIO._base._BaseExonerateParser

Parser for Exonerate plain text output.

parse_alignment_block(header)

Parse alignment block, return query result, hits, hsps.

__abstractmethods__ = frozenset({})

__annotations__ = {'_ALN_MARK': 'Optional[str]'}

class Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer(filename, **kwargs)

Bases: Bio.SearchIO.ExonerateIO._base._BaseExonerateIndexer

Indexer class for Exonerate plain text.

get_qresult_id(pos)

Return the query ID from the nearest “Query:” line.

get_raw(offset)

Return the raw string of a QueryResult object from the given offset.

__abstractmethods__ = frozenset({})

__annotations__ = {'_parser': 'Optional[Type[_BaseExonerateParser]]', '_query_mark': 'Optional[bytes]'}