Bio.SearchIO.ExonerateIO.exonerate_cigar module

Bio.SearchIO parser for Exonerate cigar output format.

class Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser(handle)

Bases: Bio.SearchIO.ExonerateIO._base._BaseExonerateParser

Parser for Exonerate cigar strings.

parse_alignment_block(header)

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

__abstractmethods__ = frozenset({})

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

class Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer(filename, **kwargs)

Bases: Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer

Indexer class for exonerate cigar lines.

get_qresult_id(pos)

Return the query ID of the nearest cigar line.

__abstractmethods__ = frozenset({})

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