Bio.SearchIO.HmmerIO.hmmer3_tab module

Bio.SearchIO parser for HMMER table output format.

class Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser(handle)

Bases: object

Parser for the HMMER table format.

__init__(self, handle)

Initialize the class.

__iter__(self)

Iterate over Hmmer3TabParser, yields query results.

class Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer(filename, **kwargs)

Bases: Bio.SearchIO._index.SearchIndexer

Indexer class for HMMER table output.

__iter__(self)

Iterate over the file handle; yields key, start offset, and length.

get_raw(self, offset)

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

class Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter(handle)

Bases: object

Writer for hmmer3-tab output format.

__init__(self, handle)

Initialize the class.

write_file(self, qresults)

Write to the handle.

Returns a tuple of how many QueryResult, Hit, and HSP objects were written.