# Bio.SearchIO.HmmerIO.hmmer2_text module

Bio.SearchIO parser for HMMER 2 text output.

class Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser(handle)

  Bases: `object`

  Iterator for the HMMER 2.0 text output.

  __init__(handle)

    Initialize the class.

  __iter__()

    Iterate over Hmmer2TextParser, yields query results.

  read_next(rstrip=True)

    Return the next non-empty line, trailing whitespace removed.

  push_back(line)

    Un-read a line that should not be parsed yet.

  parse_key_value()

    Parse key-value pair separated by colon.

  parse_preamble()

    Parse HMMER2 preamble.

  parse_qresult()

    Parse a HMMER2 query block.

  parse_hits()

    Parse a HMMER2 hit block, beginning with the hit table.

  parse_hsps(hit_placeholders)

    Parse a HMMER2 hsp block, beginning with the hsp table.

  parse_hsp_alignments()

    Parse a HMMER2 HSP alignment block.

  __firstlineno__ = 36
  __static_attributes__ = ('_meta', 'buf', 'handle', 'line', 'qresult')

class Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer(*args, **kwargs)

  Bases: `_BaseHmmerTextIndexer`

  Indexer for hmmer2-text format.

  qresult_start = b'Query'
  qresult_end = b'//'
  __iter__()

    Iterate over Hmmer2TextIndexer; yields query results’ key, offsets, 0.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 330
  __static_attributes__ = ()

Biopython v: 1.85

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