Mercurial > repos > rliterman > csp2
diff CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pybedtools/filenames.py @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author | jpayne |
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date | Tue, 18 Mar 2025 16:23:26 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pybedtools/filenames.py Tue Mar 18 16:23:26 2025 -0400 @@ -0,0 +1,47 @@ +""" +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)