Bio.SearchIO.ExonerateIO.exonerate_vulgar module
Bio.SearchIO parser for Exonerate vulgar output format.
- class Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser(handle)
Bases:
_BaseExonerateParser
Parser for Exonerate vulgar strings.
- parse_alignment_block(header)
Parse alignment block for vulgar format, return query results, hits, hsps.
- __abstractmethods__ = frozenset({})
- class Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer(filename, **kwargs)
Bases:
_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]'}