augur.io.file module

augur.io.file.create_parent_directories(file)

Create missing parent directories for path-like files.

>>> import tempfile
>>> path = tempfile.mkdtemp() + "/nested/output.txt"
>>> create_parent_directories(path)
>>> os.path.isdir(os.path.dirname(path))
True

augur.io.file.is_write_mode(mode)

Return whether mode is a write mode.

Only modes containing "w" or "a" are treated as write modes. Exclusive creation mode "x" is intentionally excluded because xopen does not support it.

Examples

>>> is_write_mode("w")
True
>>> is_write_mode("wb")
True
>>> is_write_mode("a")
True
>>> is_write_mode("r")
False
>>> is_write_mode("x")
False

augur.io.file.open_file(path_or_buffer, mode='r', **kwargs)

Opens a given file path and returns the handle.

Transparently handles compressed inputs and outputs.

Parameters:

• path_or_buffer -- Name of the file to open or an existing IO buffer

• mode (str) -- Mode to open file (read or write)

Returns:

File handle object

Return type:

IO

Examples

Pass through an existing buffer unchanged.

>>> from io import StringIO
>>> buf = StringIO("hello")
>>> with open_file(buf) as handle:
...     handle.read()
'hello'

Open a normal text file. Parent directories are created.

>>> from tempfile import TemporaryDirectory
>>> from pathlib import Path
>>> with TemporaryDirectory() as d:
...     parent = Path(d) / "nested"
...     path = parent / "example.txt"
...     with open_file(path, mode="w") as handle:
...         _ = handle.write("hello")
...     path.read_text(encoding=ENCODING)
...     parent.exists()
'hello'
True

‘x’ mode is not supported.

>>> with TemporaryDirectory() as d:
...     parent = Path(d) / "nested"
...     path = parent / "example.txt"
...     try:
...         with open_file(path, mode="x") as handle:
...             _ = handle.write("hello")
...     except ValueError as e:
...         print(e)
...     parent.exists()
Mode 'x' not supported
False