Package Bio :: Package SearchIO :: Module BlatIO :: Class BlatPslIndexer

Class BlatPslIndexer

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

Indexer class for BLAT PSL output.

Nested Classes

[hide private]

_parser
Parser for the BLAT PSL format.

Instance Methods

[hide private]

__init__(self, filename, pslx=False)
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

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

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, pslx=False)
(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 BlatPslIndexer

__init__(self, filename, pslx=False) (Constructor)

__iter__(self)

get_raw(self, offset)

init(self, filename, pslx=False)
(Constructor)

iter(self)