Source Code for Module Bio.SearchIO.HmmerIO._base

 1  # Copyright 2012 by Wibowo Arindrarto.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  """Bio.SearchIO base classes for HMMER-related code.""" 
 7   
 8  from Bio._py3k import _as_bytes 
 9  from Bio.SearchIO._index import SearchIndexer 
10   
11   
12 -class _BaseHmmerTextIndexer(SearchIndexer): 
13   
14      """Base indexer class for HMMER plain text output.""" 
15   
16 -    def __init__(self, *args, **kwargs): 
17          super(_BaseHmmerTextIndexer, self).__init__(*args, **kwargs) 
18          self._preamble = _as_bytes('') 
19   
20 -    def get_raw(self, offset): 
21          handle = self._handle 
22          qresult_raw = _as_bytes('') 
23   
24          # read header first 
25          if not self._preamble: 
26              handle.seek(0) 
27              while True: 
28                  line = handle.readline() 
29                  if line.startswith(self.qresult_start): 
30                      break 
31                  qresult_raw += line 
32          else: 
33              qresult_raw += self._preamble 
34   
35          # and read the qresult raw string 
36          handle.seek(offset) 
37          while True: 
38              # preserve whitespace, don't use read_forward 
39              line = handle.readline() 
40              qresult_raw += line 
41   
42              # break when we've reached qresult end 
43              if line.startswith(self.qresult_end) or not line: 
44                  break 
45   
46          return qresult_raw 
47