import tempfile
from pathlib import Path, PurePath
from typing import Union
try:
import pooch
"""
Load sample data.
"""
POOCH = pooch.create(
# Use the default cache folder for the OS
path=pooch.os_cache("bed_reader"),
# The remote data is on Github
base_url="https://raw.githubusercontent.com/"
+ "fastlmm/bed-sample-files/main/",
# If this is a development version, get the data from the master branch
version_dev="main",
# The registry specifies the files that can be fetched
env="BED_READER_DATA_DIR",
)
# Get registry file from package_data
registry_file = Path(__file__).parent / "tests/registry.txt"
# Load this registry file
POOCH.load_registry(registry_file)
except ImportError:
pooch = None
[docs]
def sample_file(filepath: Union[str, Path]) -> str:
"""
Retrieve a sample .bed file. (Also retrieves associated .fam and .bim files).
Parameters
----------
filepath
Name of the sample .bed file.
Returns
-------
str
Local name of sample .bed file.
.. note::
This function requires the :mod:`pooch` package. Install `pooch` with:
.. code-block:: bash
pip install --upgrade bed-reader[samples]
By default this function puts files under the user's cache directory.
Override this by setting
the `BED_READER_DATA_DIR` environment variable.
Example
--------
.. doctest::
>>> # pip install bed-reader[samples] # if needed
>>> from bed_reader import sample_file
>>>
>>> file_name = sample_file("small.bed")
>>> print(f"The local file name is '{file_name}'")
The local file name is '...small.bed'
"""
if pooch is None:
raise ImportError(
"The function sample_file() requires pooch. "
+ "Install it with 'pip install --upgrade bed-reader[samples]'."
)
filepath = Path(filepath)
file_string = str(filepath)
if file_string.lower().endswith(".bed"):
POOCH.fetch(file_string[:-4] + ".fam")
POOCH.fetch(file_string[:-4] + ".bim")
return POOCH.fetch(file_string)
def sample_url(filepath: Union[str, Path]) -> str:
"""
Retrieve a URL to a sample .bed file. (Also makes ready associated .fam and .bim files).
Parameters
----------
filepath
Name of the sample .bed file.
Returns
-------
str
URL to sample .bed file.
.. note::
This function requires the :mod:`pooch` package. Install `pooch` with:
.. code-block:: bash
pip install --upgrade bed-reader[samples]
By default this function puts files under the user's cache directory.
Override this by setting
the `BED_READER_DATA_DIR` environment variable.
Example
--------
.. doctest::
>>> # pip install bed-reader[samples] # if needed
>>> from bed_reader import sample_url
>>>
>>> url = sample_url("small.bed")
>>> print(f"The url is '{url}'")
The url is 'file:///.../small.bed'
"""
file_name = sample_file(filepath)
url = PurePath(file_name).as_uri()
return url
[docs]
def tmp_path() -> Path:
"""
Return a :class:`pathlib.Path` to a temporary directory.
Returns
-------
pathlib.Path
a temporary directory
Example
--------
.. doctest::
>>> from bed_reader import to_bed, tmp_path
>>>
>>> output_file = tmp_path() / "small3.bed"
>>> val = [[1, 0, -127, 0], [2, 0, -127, 2], [0, 1, 2, 0]]
>>> to_bed(output_file, val)
"""
temp_dir = tempfile.gettempdir()
path = Path(temp_dir) / "bed_reader_tmp_path"
path.mkdir(parents=True, exist_ok=True)
return path
# if __name__ == "__main__":
# logging.basicConfig(level=logging.INFO)
# import pytest
# pytest.main(["--doctest-modules", __file__])