# Bio.SearchIO.HmmerIO.hmmer3_domtab module

Bio.SearchIO parser for HMMER domain table output format.

class Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser(handle)

  Bases: `Hmmer3DomtabParser`

  HMMER domain table parser using hit coordinates.

  Parser for the HMMER domain table format that assumes HMM profile coordinates are hit coordinates.

  hmm_as_hit = True
  __firstlineno__ = 167
  __static_attributes__ = ()

class Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser(handle)

  Bases: `Hmmer3DomtabParser`

  HMMER domain table parser using query coordinates.

  Parser for the HMMER domain table format that assumes HMM profile coordinates are query coordinates.

  hmm_as_hit = False
  __annotations__ = {}
  __firstlineno__ = 177
  __static_attributes__ = ()

class Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer(filename, **kwargs)

  Bases: `Hmmer3TabIndexer`

  HMMER domain table indexer using hit coordinates.

  Indexer class for HMMER domain table output that assumes HMM profile coordinates are hit coordinates.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 187
  __static_attributes__ = ()

class Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer(filename, **kwargs)

  Bases: `Hmmer3TabIndexer`

  HMMER domain table indexer using query coordinates.

  Indexer class for HMMER domain table output that assumes HMM profile coordinates are query coordinates.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 198
  __static_attributes__ = ()

class Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter(handle)

  Bases: `object`

  HMMER domain table writer using hit coordinates.

  Writer for hmmer3-domtab output format which writes hit coordinates as HMM profile coordinates.

  hmm_as_hit = True
  __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__ = 209
  __static_attributes__ = ('handle',)

class Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter(handle)

  Bases: `Hmmer3DomtabHmmhitWriter`

  HMMER domain table writer using query coordinates.

  Writer for hmmer3-domtab output format which writes query coordinates as HMM profile coordinates.

  hmm_as_hit = False
  __annotations__ = {}
  __firstlineno__ = 364
  __static_attributes__ = ()

Biopython v: 1.85

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