Bio :: File :: _SQLiteManySeqFilesDict :: Class _SQLiteManySeqFilesDict

Class _SQLiteManySeqFilesDict

UserDict.DictMixin --+    
                     |    
   _IndexedSeqFileDict --+
                         |
                        _SQLiteManySeqFilesDict

Read only dictionary interface to many sequential record files.

This code is used in both Bio.SeqIO for indexing as SeqRecord
objects, and in Bio.SearchIO for indexing QueryResult objects.

Keeps the keys, file-numbers and offsets in an SQLite database. To access
a record by key, reads from the offset in the appropriate file and then
parses the record into an object.

There are OS limits on the number of files that can be open at once,
so a pool are kept. If a record is required from a closed file, then
one of the open handles is closed first.

Instance Methods

[hide private]

__init__(self, index_filename, filenames, proxy_factory, format, key_function, repr, max_open=10)

source code

__repr__(self)

source code

__contains__(self, key)

source code

__len__(self)
How many records are there?

source code

__iter__(self)
Iterate over the keys.

source code

keys(self)
Return a list of all the keys (SeqRecord identifiers).

source code

__getitem__(x, y)
x[y]

source code

D[k] if k in D, else d

get(D, k, d=...)
d defaults to None.

source code

get_raw(self, key)
Similar to the get method, but returns the record as a raw string.

source code

close(self)
Close any open file handles.

source code

Inherited from _IndexedSeqFileDict: __setitem__, __str__, clear, copy, fromkeys, items, iteritems, iterkeys, itervalues, pop, popitem, update, values

Inherited from UserDict.DictMixin: __cmp__, has_key, setdefault

Method Details

[hide private]

init(self, index_filename, filenames, proxy_factory, format, key_function, repr, max_open=10)
(Constructor)

source code

Overrides: _IndexedSeqFileDict.__init__

repr(self)
(Representation operator)

source code

Overrides: UserDict.DictMixin.__repr__

contains(self, key)
(In operator)

source code

Overrides: UserDict.DictMixin.__contains__

len(self)
(Length operator)

source code

How many records are there?

Overrides: UserDict.DictMixin.__len__

iter(self)

source code

Iterate over the keys.

Overrides: UserDict.DictMixin.__iter__

keys(self)

source code

Return a list of all the keys (SeqRecord identifiers).

Overrides: _IndexedSeqFileDict.keys

getitem(x, y)
(Indexing operator)

source code

x[y]

Overrides: _IndexedSeqFileDict.__getitem__

get(D, k, d=...)

source code

d defaults to None.

Returns: D[k] if k in D, else d
Overrides: UserDict.DictMixin.get

get_raw(self, key)

source code

Similar to the get method, but returns the record as a raw string.

If the key is not found, a KeyError exception is raised.

Note that on Python 3 a bytes string is returned, not a typical
unicode string.

NOTE - This functionality is not supported for every file format.

Overrides: _IndexedSeqFileDict.get_raw

Class _SQLiteManySeqFilesDict

__init__(self, index_filename, filenames, proxy_factory, format, key_function, repr, max_open=10) (Constructor)

__repr__(self) (Representation operator)

__contains__(self, key) (In operator)

__len__(self) (Length operator)

__iter__(self)

keys(self)

__getitem__(x, y) (Indexing operator)

get(D, k, d=...)

get_raw(self, key)

init(self, index_filename, filenames, proxy_factory, format, key_function, repr, max_open=10)
(Constructor)

repr(self)
(Representation operator)

contains(self, key)
(In operator)

len(self)
(Length operator)

iter(self)

getitem(x, y)
(Indexing operator)