Source Code for Module Bio.SearchIO._index

 1  # Copyright 2012 by Wibowo Arindrarto.  All rights reserved. 
 2  # All rights reserved. 
 3  # This code is part of the Biopython distribution and governed by its 
 4  # license.  Please see the LICENSE file that should have been included 
 5  # as part of this package. 
 6   
 7  #TODO: factor out this module with SeqIO's _index to stay DRY 
 8   
 9  """Custom indexing for Bio.SearchIO objects.""" 
10   
11  from StringIO import StringIO 
12  from Bio._py3k import _bytes_to_string 
13  from Bio import bgzf 
14  from Bio.File import _IndexedSeqFileProxy, _open_for_random_access 
15   
16   
17 -class SearchIndexer(_IndexedSeqFileProxy): 
18      """Base class for file format specific random access. 
19   
20      Subclasses for each file format should define '_parser' and optionally 
21      'get_raw' methods. 
22      """ 
23   
24 -    def __init__(self, filename, **kwargs): 
25          self._handle = _open_for_random_access(filename) 
26          self._kwargs = kwargs 
27   
28 -    def _parse(self, handle): 
29          return iter(self._parser(handle, **self._kwargs)).next() 
30   
31 -    def get(self, offset): 
32          return self._parse(StringIO(_bytes_to_string(self.get_raw(offset)))) 
33