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pybedtools.bedtool.BedTool.save_seqs leaves open .tmp files #381

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PeterRobots opened this issue Jan 19, 2023 · 0 comments
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pybedtools.bedtool.BedTool.save_seqs leaves open .tmp files #381

PeterRobots opened this issue Jan 19, 2023 · 0 comments

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@PeterRobots
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A warning is generated when using the command on a sequence.
Found when running unittests.

Python==3.8.0
async-timeout==4.0.2
attrs==22.2.0
biopython==1.79
certifi==2022.12.7
charset-normalizer==3.0.1
click==8.1.3
Cython==0.29.30
Deprecated==1.2.13
docker==5.0.3
exceptiongroup==1.1.0
Flask==2.2.2
idna==3.4
importlib-metadata==6.0.0
iniconfig==2.0.0
itsdangerous==2.1.2
Jinja2==3.1.2
MarkupSafe==2.1.2
mock==4.0.3
numpy==1.24.1
packaging==23.0
pkg_resources==0.0.0
pluggy==1.0.0
primer3-py==0.6.1
pybedtools==0.9.0
pycodestyle==2.9.1
pyfakefs==4.6.2
pysam==0.16.0.1
pytest==7.2.1
redis==4.3.3
requests==2.28.2
six==1.16.0
tomli==2.0.1
urllib3==1.26.14
websocket-client==1.4.2
Werkzeug==2.2.2
wrapt==1.14.1
zipp==3.11.0

It's resolved by closing self.seqfn after reading and writing to fout.

PeterRobots pushed a commit to PeterRobots/pybedtools that referenced this issue Jan 19, 2023
PeterRobots added a commit to PeterRobots/pybedtools that referenced this issue Jan 25, 2023
Fixes daler#381 closes all .tmp files opened by .save_seqs
daler added a commit that referenced this issue Jul 1, 2023
Co-authored-by: Peter Inzani <pi2@sanger.ac.uk>
Co-authored-by: Ryan Dale <ryan.dale@nih.gov>
@daler daler closed this as completed in 96e271d Aug 13, 2023
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