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| # Copyright 2012 by Wibowo Arindrarto. All rights reserved. | |
| # Revisions copyright 2012-2016 by Peter Cock. All rights reserved. | |
| # | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Custom indexing for Bio.SearchIO objects.""" | |
| from io import StringIO | |
| from Bio.File import _IndexedSeqFileProxy, _open_for_random_access | |
| class SearchIndexer(_IndexedSeqFileProxy): | |
| """Base class for file format specific random access. | |
| Subclasses for each file format should define '_parser' and optionally | |
| 'get_raw' methods. | |
| """ | |
| def __init__(self, filename, **kwargs): | |
| """Initialize the class.""" | |
| self._handle = _open_for_random_access(filename) | |
| self._kwargs = kwargs | |
| def _parse(self, handle): | |
| """Pass handle and arguments to the next iterable (PRIVATE).""" | |
| return next(iter(self._parser(handle, **self._kwargs))) | |
| def get(self, offset): | |
| """Get offset and convert it from bytes to string.""" | |
| return self._parse(StringIO(self.get_raw(offset).decode())) | |