Resolved #19 added docstring, fixed nproc and removed depth function #29
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…nformation" This reverts commit ca64a2f.
…emoved depth function
…s and renamed stderr and stdout
…ed additional line in the end, and used o.path.dirname(os.path.abspath(otput.bam))
…r is nproc not int
autometa/common/external/samtools.py
Outdated
| retcode = subprocess.call(cmd, stdout=stdout, stderr=stderr, shell=True) | ||
| if retcode != 0: | ||
| shutil.rmtree(tempdir, ignore_errors=True) | ||
| raise ChildProcessError(f'Sort failed, retcode: {retcode}') | ||
| else: | ||
| shutil.move(temp_outfile, samtools_outfile) |
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This will work in according to the behavior we expect for the program, however, if a different exception is raised (for example the user kills the pipeline) will the temporary directory remain? We also need to account for unexpected behavior, which can be difficult due to the nature of the issue, although try/except/finally and specific exception handling can help assess any of the known issues to provide some clarity to the unknown issues.
You might be able to achieve the required behavior (unsure about the exception handling) strictly using the TemporaryDirectory function from the built-in tempfile library.
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I can check for FileNotFoundError (the same way I am checking if nproc > 0) but I am not exactly sure what all other errors might we encounter and how can we catch-all of them individually.
Won't they be recorded in samtool.err file?
Issues resolved:
depthfunction was not being called from any other script. The function is supposed to use samtools to compute the read depth at each position or region, however, it is not being implemented anywhere. It was removed after consulting with @WiscEvan.nprocwas changed tomp.cpu_count()it now uses all the processors in the system as a default option.runfunction more intuitive. Changes here might affect coverage.py file as the function is being called there.