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"""
Provides access to example files and keeps track of all temp files created
during a Python session.
"""
import os
TEMPFILES = []
def data_dir():
"""
Returns the data directory that contains example files for tests and
documentation.
"""
return os.path.join(os.path.dirname(__file__), "test", "data")
def example_filename(fn):
"""
Return a bed file from the pybedtools examples directory. Use
func:`list_example_files` to see a list of files that are included.
"""
fn = os.path.join(data_dir(), fn)
if not os.path.exists(fn):
msg = "%s does not exist" % fn
raise FileNotFoundError(msg)
return fn
def list_example_files():
"""
Returns a list of files in the examples dir. Choose one and pass it to
:func:`example_filename` to get the full path to an example file.
Example usage:
>>> from pybedtools import BedTool
>>> choices = list_example_files()
>>> assert 'a.bed' in choices
>>> bedfn = example_filename('a.bed')
>>> mybedtool = BedTool(bedfn)
"""
candidate_fns = os.listdir(data_dir())
exts = (".bed", ".gff", ".gtf", ".bed.gz", ".bam", ".gff.gz")
valid_fns = [f for f in candidate_fns if f.endswith(exts)]
return sorted(valid_fns)
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