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

Class BlastTabIndexer

               object --+        
                        |        
File._IndexedSeqFileProxy --+    
                            |    
         _index.SearchIndexer --+
                                |
                               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 x.__class__.__doc__ for signature source code

__iter__(self)
Iterates over the file handle; yields key, start offset, and length.

source code

_qresult_index_commented(self)
Indexer for commented BLAST tabular files.

source code

_qresult_index(self)
Indexer for noncommented BLAST tabular files.

source code

get_raw(self, offset)
Returns the raw string of a QueryResult object from the given offset.

source code

_get_raw_qresult(self, offset)
Returns the raw string of a single QueryResult from a noncommented file.

source code

_get_raw_qresult_commented(self, offset)
Returns the raw string of a single QueryResult from a commented file.

source code

Inherited from _index.SearchIndexer: get

Inherited from _index.SearchIndexer (private): _parse

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

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

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

iter(self)

source code

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

Overrides: File._IndexedSeqFileProxy.__iter__

get_raw(self, offset)

source code

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

Overrides: File._IndexedSeqFileProxy.get_raw

Class BlastTabIndexer

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

__iter__(self)

get_raw(self, offset)

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

iter(self)