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pyani listdeps broken :: pyani/aniblastall.py :: blastall doe not have --version option

See original GitHub issue

Summary:

running pyany listdeps from fresh cloned repo (commit 0081885c0c5c81e6885a533279c56749c5c12bd4) I have the following error

Installed third-party tool versions...
	blast+==Linux_2.10.0+
	nucmer==Linux_3.1
Traceback (most recent call last):
  File "/opt/gensoft/exe/pyani/0.3.0a0/bin/pyani", line 8, in <module>
    sys.exit(run_main())
  File "/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages/pyani/scripts/pyani_script.py", line 105, in run_main
    returnval = args.func(args)
  File "/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages/pyani/scripts/subcommands/subcmd_listdeps.py", line 86, in subcmd_listdeps
    for tool, version in get_tool_versions():
  File "/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages/pyani/dependencies.py", line 117, in get_tool_versions
    yield (name, func())
  File "/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages/pyani/aniblastall.py", line 74, in get_version
    version = re.search(  # type: ignore
AttributeError: 'NoneType' object has no attribute 'group'

pyani Version:

pyani does not provide a way to know his version 😉 a --version flag will be nice.

anyway

average_nucleotide_identity.py --version 
average_nucleotide_identity.py: pyani 0.3.0-alpha

code clone from commit 0081885c0c5c81e6885a533279c56749c5c12bd4

installed dependencies

If you are running a version of pyani v0.3 or later, then please run the command pyani listdeps at the command line, and enter the output below.

see above problem 😉

System information
        Platorm==Linux-4.18.0-193.19.1.el8_2.x86_64-x86_64-with-glibc2.2.5
        Python==3.8.1 (default, May 22 2020, 14:09:57)
[GCC 9.2.0]
Installed pyani Python dependendencies...
        Pillow==8.1.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        biopython==1.78 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        matplotlib==3.3.3 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        namedlist==1.8 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        networkx==2.5 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        numpy==1.19.5 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        openpyxl==Not Installed (-)
        pandas==1.2.1 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        scipy==1.6.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        seaborn==0.11.1 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        sqlalchemy==1.3.22 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
        tqdm==4.56.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
Installed pyani development dependendencies...
        bandit==Not Installed (-)
        black==Not Installed (-)
        coverage==Not Installed (-)
        doc8==Not Installed (-)
        flake8==Not Installed (-)
        jinja2==Not Installed (-)
        mypy==Not Installed (-)
        pydocstyle==Not Installed (-)
        pylint==Not Installed (-)
        pytest==Not Installed (-)
        pytest-cov==Not Installed (-)
        sphinx==Not Installed (-)
Installed pyani pip-install dependendencies...
        pre-commit==Not Installed (-)
        pytest-ordering==Not Installed (-)
        sphinx-rtd-theme==Not Installed (-)
Installed third-party tool versions...
        blast+==Linux_2.10.0+
        nucmer==Linux_3.1
Traceback (most recent call last):
  File "/opt/gensoft/exe/pyani/0.3.0a0/bin/pyani", line 8, in <module>
    sys.exit(run_main())
  File "/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages/pyani/scripts/pyani_script.py", line 105, in run_main
    returnval = args.func(args)
  File "/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages/pyani/scripts/subcommands/subcmd_listdeps.py", line 86, in subcmd_listdeps
    for tool, version in get_tool_versions():
  File "/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages/pyani/dependencies.py", line 117, in get_tool_versions
    yield (name, func())
  File "/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages/pyani/aniblastall.py", line 74, in get_version
    version = re.search(  # type: ignore
AttributeError: 'NoneType' object has no attribute 'group'

problem is that blastall does not provide a --version option. when called blastall --version it display an error message. tested with legacy blast 2.2.19, 2.2.21, 2.2.25, 2.2.26.

tars-submit0:~ > blastall --version 
[blastall] ERROR: Invalid argument: --version

it should be called with --help instead of --version

furthermore blastall output in this case is deirected to stdout not stderr

changing code from

This is concatenated with the OS name.
    """
    cmdline = [blast_exe, "-version"]
    result = subprocess.run(
        cmdline,  # type: ignore
        shell=False,
        stdout=subprocess.PIPE,  # type: ignore
        stderr=subprocess.PIPE,
        check=False,  # blastall doesn't return 0
    )
    version = re.search(  # type: ignore
        r"(?<=blastall\s)[0-9\.]*", str(result.stderr, "utf-8")
    ).group()

to

    This is concatenated with the OS name.
    """
    cmdline = [blast_exe, '--help']
    result = subprocess.run(
        cmdline,  # type: ignore
        shell=False,
        stdout=subprocess.PIPE,  # type: ignore
        stderr=subprocess.PIPE,
        check=False,  # blastall doesn't return 0
    )
    
    version = re.search(  # type: ignore
        r"(?<=blastall\s)[0-9\.]*", str(result.stdout, "utf-8")

fix the problem see:

pyani listdeps 2>&1| tee log
System information
	Platorm==Linux-4.18.0-193.19.1.el8_2.x86_64-x86_64-with-glibc2.2.5
	Python==3.8.1 (default, May 22 2020, 14:09:57) 
[GCC 9.2.0]
Installed pyani Python dependendencies...
	Pillow==8.1.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	biopython==1.78 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	matplotlib==3.3.3 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	namedlist==1.8 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	networkx==2.5 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	numpy==1.19.5 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	openpyxl==Not Installed (-)
	pandas==1.2.1 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	scipy==1.6.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	seaborn==0.11.1 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	sqlalchemy==1.3.22 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	tqdm==4.56.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
Installed pyani development dependendencies...
	bandit==Not Installed (-)
	black==Not Installed (-)
	codecov==Not Installed (-)
	coverage==Not Installed (-)
	doc8==Not Installed (-)
	flake8==Not Installed (-)
	jinja2==Not Installed (-)
	mypy==Not Installed (-)
	pydocstyle==Not Installed (-)
	pylint==Not Installed (-)
	pytest==Not Installed (-)
	pytest-cov==Not Installed (-)
	sphinx==Not Installed (-)
Installed pyani pip-install dependendencies...
	pre-commit==Not Installed (-)
	pytest-ordering==Not Installed (-)
	sphinx-rtd-theme==Not Installed (-)
Installed third-party tool versions...
	blast+==Linux_2.10.0+
	nucmer==Linux_3.1
	blastall==Linux_2.2.26
[gensoft@345ddfccadad pyani-0.3.0a0]$ 
[gensoft@345ddfccadad pyani-0.3.0a0]$ pyani listdeps 2>&1| tee log
System information
	Platorm==Linux-4.18.0-193.19.1.el8_2.x86_64-x86_64-with-glibc2.2.5
	Python==3.8.1 (default, May 22 2020, 14:09:57) 
[GCC 9.2.0]
Installed pyani Python dependendencies...
	Pillow==8.1.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	biopython==1.78 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	matplotlib==3.3.3 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	namedlist==1.8 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	networkx==2.5 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	numpy==1.19.5 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	openpyxl==Not Installed (-)
	pandas==1.2.1 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	scipy==1.6.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	seaborn==0.11.1 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	sqlalchemy==1.3.22 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
	tqdm==4.56.0 (/opt/gensoft/exe/pyani/0.3.0a0/venv/lib/python3.8/site-packages)
Installed pyani development dependendencies...
	bandit==Not Installed (-)
	black==Not Installed (-)
	codecov==Not Installed (-)
	coverage==Not Installed (-)
	doc8==Not Installed (-)
	flake8==Not Installed (-)
	jinja2==Not Installed (-)
	mypy==Not Installed (-)
	pydocstyle==Not Installed (-)
	pylint==Not Installed (-)
	pytest==Not Installed (-)
	pytest-cov==Not Installed (-)
	sphinx==Not Installed (-)
Installed pyani pip-install dependendencies...
	pre-commit==Not Installed (-)
	pytest-ordering==Not Installed (-)
	sphinx-rtd-theme==Not Installed (-)
Installed third-party tool versions...
	blast+==Linux_2.10.0+
	nucmer==Linux_3.1
	blastall==Linux_2.2.26

hope this will help

regards

Eric

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:5 (5 by maintainers)

github_iconTop GitHub Comments

1reaction
baileythegreencommented, Apr 21, 2021

pyani Version:

pyani does not provide a way to know his version 😉 a --version flag will be nice.

This is fixed in #263. (But also, running just pyani outputs it in version 0.3.0a0, which is the version number shows up in your traceback.

@widdowquinn None of the subcommands seem to have a working --version flag, despite collecting version information; I’ll see about adding that to #263.

0reactions
widdowquinncommented, Apr 21, 2021

Are the two options you’re proposing mutually exclusive alternatives? The first one might be good to include more generally (not just for blastall), in case something can’t be found.

No - I’m implicitly going for “can’t find blastall” and the like with (1); (2) is just to account for how we need to call blastall.

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