Bio.SearchIO.ExonerateIO.exonerate_vulgar module

Bio.SearchIO parser for Exonerate vulgar output format.

class Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser(handle)

Bases: Bio.SearchIO.ExonerateIO._base._BaseExonerateParser

Parser for Exonerate vulgar strings.

parse_alignment_block(header)

Parse alignment block for vulgar format, return query results, hits, hsps.

__abstractmethods__ = frozenset({})

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

class Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer(filename, **kwargs)

Bases: Bio.SearchIO.ExonerateIO._base._BaseExonerateIndexer

Indexer class for exonerate vulgar lines.

get_qresult_id(pos)

Return the query ID of the nearest vulgar line.

get_raw(offset)

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

__abstractmethods__ = frozenset({})

__annotations__ = {'_parser': typing.Type[Bio.SearchIO.ExonerateIO._base._BaseExonerateParser], '_query_mark': 'Optional[bytes]'}