Bio.File module

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.

Bio.File.as_handle(handleish, mode='r', **kwargs)

Context manager to ensure we are using a handle.

Context manager for arguments that can be passed to SeqIO and AlignIO read, write, and parse methods: either file objects or path-like objects (strings, pathlib.Path instances, or more generally, anything that can be handled by the builtin ‘open’ function).

When given a path-like object, returns an open file handle to that path, with provided mode, which will be closed when the manager exits.

All other inputs are returned, and are not closed.

Arguments:
  • handleish - Either a file handle or path-like object (anything which can be

    passed to the builtin ‘open’ function: str, bytes, and under Python >= 3.6, pathlib.Path, os.DirEntry)

  • mode - Mode to open handleish (used only if handleish is a string)

  • kwargs - Further arguments to pass to open(…)

Examples

>>> from Bio import File
>>> with File.as_handle('seqs.fasta', 'w') as fp:
...     # Python2/3 docstring workaround, revise for 'Python 3 only'.
...     _ = fp.write('>test\nACGT')
...
>>> fp.closed
True

>>> handle = open('seqs.fasta', 'w')
>>> with File.as_handle(handle) as fp:
...     # Python 2/3 docstring workaround, revise for 'Python 3 only'.
...     _ = fp.write('>test\nACGT')
...
>>> fp.closed
False
>>> fp.close()

Note that if the mode argument includes U (for universal new lines) this will be removed under Python 3 where is is redundant and has been deprecated (this happens automatically in text mode).

class Bio.File.UndoHandle(handle)

Bases: object

A Python handle that adds functionality for saving lines.

Saves lines in a LIFO fashion.

Added methods:

  • saveline Save a line to be returned next time.

  • peekline Peek at the next line without consuming it.

__init__(self, handle)

Initialize the class.

__iter__(self)

Iterate over the lines in the File.

__next__(self)

Return the next line.

readlines(self, *args, **keywds)

Read all the lines from the file as a list of strings.

readline(self, *args, **keywds)

Read the next line from the file as string.

read(self, size=- 1)

Read the File.

saveline(self, line)

Store a line in the cache memory for later use.

This acts to undo a readline, reflecting the name of the class: UndoHandle.

peekline(self)

Return the next line in the file, but do not move forward though the file.

tell(self)

Return the current position of the file read/write pointer within the File.

seek(self, *args)

Set the current position at the offset specified.

__getattr__(self, attr)

Return File attribute.

__enter__(self)

Call special method when opening the file using a with-statement.

__exit__(self, type, value, traceback)

Call special method when closing the file using a with-statement.