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