Bio.File module

Code for more fancy file handles.

Bio.File defines private classes used in Bio.SeqIO and Bio.SearchIO for indexing files. 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, such as str, bytes, pathlib.Path, and os.DirEntry objects)

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

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

Examples

>>> from Bio import File
>>> import os
>>> with File.as_handle('seqs.fasta', 'w') as fp:
...     fp.write('>test\nACGT')
...
10
>>> fp.closed
True

>>> handle = open('seqs.fasta', 'w')
>>> with File.as_handle(handle) as fp:
...     fp.write('>test\nACGT')
...
10
>>> fp.closed
False
>>> fp.close()
>>> os.remove("seqs.fasta")  # tidy up