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.
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.
- 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(…)
>>> 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
A Python handle that adds functionality for saving lines (DEPRECATED).
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.
Initialize the class.