# 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.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __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({})
  __annotate_func__ = None
  __annotations_cache__ = {}
  __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.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 217
  __static_attributes__ = ('handle',)

Biopython v: 1.86

Versions
  Previous
  Latest
  Develop

Biopython Project
  Homepage
  On GitHub