Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pybedtools/filenames.py @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
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| children |
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| 67:0e9998148a16 | 68:5028fdace37b |
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| 1 """ | |
| 2 Provides access to example files and keeps track of all temp files created | |
| 3 during a Python session. | |
| 4 """ | |
| 5 import os | |
| 6 | |
| 7 TEMPFILES = [] | |
| 8 | |
| 9 | |
| 10 def data_dir(): | |
| 11 """ | |
| 12 Returns the data directory that contains example files for tests and | |
| 13 documentation. | |
| 14 """ | |
| 15 return os.path.join(os.path.dirname(__file__), "test", "data") | |
| 16 | |
| 17 | |
| 18 def example_filename(fn): | |
| 19 """ | |
| 20 Return a bed file from the pybedtools examples directory. Use | |
| 21 func:`list_example_files` to see a list of files that are included. | |
| 22 """ | |
| 23 fn = os.path.join(data_dir(), fn) | |
| 24 if not os.path.exists(fn): | |
| 25 msg = "%s does not exist" % fn | |
| 26 raise FileNotFoundError(msg) | |
| 27 return fn | |
| 28 | |
| 29 | |
| 30 def list_example_files(): | |
| 31 """ | |
| 32 Returns a list of files in the examples dir. Choose one and pass it to | |
| 33 :func:`example_filename` to get the full path to an example file. | |
| 34 | |
| 35 Example usage: | |
| 36 | |
| 37 >>> from pybedtools import BedTool | |
| 38 >>> choices = list_example_files() | |
| 39 >>> assert 'a.bed' in choices | |
| 40 >>> bedfn = example_filename('a.bed') | |
| 41 >>> mybedtool = BedTool(bedfn) | |
| 42 | |
| 43 """ | |
| 44 candidate_fns = os.listdir(data_dir()) | |
| 45 exts = (".bed", ".gff", ".gtf", ".bed.gz", ".bam", ".gff.gz") | |
| 46 valid_fns = [f for f in candidate_fns if f.endswith(exts)] | |
| 47 return sorted(valid_fns) |