Package Bio :: Module File
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Module File

source code

Code for more fancy file handles.


Classes:

UndoHandle     File object decorator with support for undo-like operations.

Additional private classes used in Bio.SeqIO and Bio.SearchIO for indexing
files are also defined under Bio.File but these are not intended for direct
use.

Classes [hide private]
  UndoHandle
A Python handle that adds functionality for saving lines.
  _IndexedSeqFileProxy
Base class for file format specific random access (PRIVATE).
  _IndexedSeqFileDict
Read only dictionary interface to a sequential record file.
  _SQLiteManySeqFilesDict
Read only dictionary interface to many sequential record files.
Functions [hide private]
 
as_handle(*args, **kwds)
Context manager for arguments that can be passed to SeqIO and AlignIO read, write, and parse methods: either file objects or strings.
source code
 
_open_for_random_access(filename)
Open a file in binary mode, spot if it is BGZF format etc (PRIVATE).
source code
Variables [hide private]
  __package__ = 'Bio'
Function Details [hide private]

as_handle(*args, **kwds)

source code 

    Context manager for arguments that can be passed to
    SeqIO and AlignIO read, write, and parse methods: either file objects or strings.

    When given a string, returns a file handle open to handleish with provided
    mode which will be closed when the manager exits.

    All other inputs are returned, and are *not* closed

    - handleish  - Either a string or file handle
    - mode       - Mode to open handleish (used only if handleish is a string)
    - kwargs     - Further arguments to pass to open(...)

    Example:

    >>> with as_handle('seqs.fasta', 'w') as fp:
    ...     fp.write('>test
ACGT')
    >>> fp.closed
    True

    >>> handle = open('seqs.fasta', 'w')
    >>> with as_handle(handle) as fp:
    ...     fp.write('>test
ACGT')
    >>> fp.closed
    False
    >>> fp.close()
    

Decorators:
  • @contextlib.contextmanager

_open_for_random_access(filename)

source code 
Open a file in binary mode, spot if it is BGZF format etc (PRIVATE).

This funcationality is used by the Bio.SeqIO and Bio.SearchIO index
and index_db functions.