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

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

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({})

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({})

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.

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