Package Bio :: Package SearchIO :: Package BlastIO :: Module blast_tab :: Class BlastTabIndexer
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Class BlastTabIndexer

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               object --+        
                        |        
File._IndexedSeqFileProxy --+    
                            |    
         _index.SearchIndexer --+
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                               BlastTabIndexer

Indexer class for BLAST+ tab output.

Nested Classes [hide private]
  _parser
Parser for the BLAST tabular format.
Instance Methods [hide private]
 
__init__(self, filename, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen'...)
x.__init__(...) initializes x; see help(type(x)) for signature
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__iter__(self)
Iterates over the file handle; yields key, start offset, and length.
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_qresult_index_commented(self)
Indexer for commented BLAST tabular files.
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_qresult_index(self)
Indexer for noncommented BLAST tabular files.
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get_raw(self, offset)
Returns the raw string of a QueryResult object from the given offset.
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_get_raw_qresult(self, offset)
Returns the raw string of a single QueryResult from a noncommented file.
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_get_raw_qresult_commented(self, offset)
Returns the raw string of a single QueryResult from a commented file.
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Inherited from _index.SearchIndexer: get

Inherited from _index.SearchIndexer (private): _parse

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, filename, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen'...)
(Constructor)

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x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

__iter__(self)

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Iterates over the file handle; yields key, start offset, and length.

Overrides: File._IndexedSeqFileProxy.__iter__

get_raw(self, offset)

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Returns the raw string of a QueryResult object from the given offset.

Overrides: File._IndexedSeqFileProxy.get_raw