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