Package Bio :: Module File

Module File

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

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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

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

source code

Function Details

[hide private]

_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.