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__(handle)
Initialize the class.
- __iter__()
Iterate over Hmmer3TabParser, yields query results.
- __annotations__ = {}
- __firstlineno__ = 19
- __static_attributes__ = ('handle', 'line')
- class Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer(filename, **kwargs)
Bases:
SearchIndexer
Indexer class for HMMER table output.
- __iter__()
Iterate over the file handle; yields key, start offset, and length.
- get_raw(offset)
Return the raw bytes string of a QueryResult object from the given offset.
- __abstractmethods__ = frozenset({})
- __annotations__ = {}
- __firstlineno__ = 145
- __static_attributes__ = ()
- class Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter(handle)
Bases:
object
Writer for hmmer3-tab output format.
- __init__(handle)
Initialize the class.
- write_file(qresults)
Write to the handle.
Returns a tuple of how many QueryResult, Hit, and HSP objects were written.
- __firstlineno__ = 217
- __static_attributes__ = ('handle',)