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({})

__annotate_func__ = <function _BaseExonerateParser.__annotate__>

__annotations_cache__ = {'_ALN_MARK': 'str | None'}

__firstlineno__ = 123

__static_attributes__ = ()

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({})

__annotate_func__()

The type of the None singleton.

__annotations_cache__ = {'_parser': type[Bio.SearchIO.ExonerateIO._base._BaseExonerateParser], '_query_mark': 'bytes | None'}

__firstlineno__ = 176

__static_attributes__ = ()