Bio.SearchIO.HmmerIO.hmmer3_domtab module¶
Bio.SearchIO parser for HMMER domain table output format.
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class
Bio.SearchIO.HmmerIO.hmmer3_domtab.
Hmmer3DomtabHmmhitParser
(handle)¶ Bases:
Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabParser
HMMER domain table parser using hit coordinates.
Parser for the HMMER domain table format that assumes HMM profile coordinates are hit coordinates.
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hmm_as_hit
= True¶
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class
Bio.SearchIO.HmmerIO.hmmer3_domtab.
Hmmer3DomtabHmmqueryParser
(handle)¶ Bases:
Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabParser
HMMER domain table parser using query coordinates.
Parser for the HMMER domain table format that assumes HMM profile coordinates are query coordinates.
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hmm_as_hit
= False¶
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class
Bio.SearchIO.HmmerIO.hmmer3_domtab.
Hmmer3DomtabHmmhitIndexer
(filename, **kwargs)¶ Bases:
Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer
HMMER domain table indexer using hit coordinates.
Indexer class for HMMER domain table output that assumes HMM profile coordinates are hit coordinates.
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__abstractmethods__
= frozenset({})¶
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class
Bio.SearchIO.HmmerIO.hmmer3_domtab.
Hmmer3DomtabHmmqueryIndexer
(filename, **kwargs)¶ Bases:
Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer
HMMER domain table indexer using query coordinates.
Indexer class for HMMER domain table output that assumes HMM profile coordinates are query coordinates.
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__abstractmethods__
= frozenset({})¶
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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.
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hmm_as_hit
= True¶
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__init__
(self, handle)¶ Initialize the class.
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write_file
(self, qresults)¶ Write to the handle.
Returns a tuple of how many QueryResult, Hit, and HSP objects were written.
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class
Bio.SearchIO.HmmerIO.hmmer3_domtab.
Hmmer3DomtabHmmqueryWriter
(handle)¶ Bases:
Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter
HMMER domain table writer using query coordinates.
Writer for hmmer3-domtab output format which writes query coordinates as HMM profile coordinates.
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hmm_as_hit
= False¶
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