Problems running any of the tools due to PyVCF

[bozbezbozzel]

• pvactools version: 3.1.9
• Python version: 3.7.12
• Operating System: Ubuntu

Describe the bug

Cannot run pvacseq due to weird errors that are very likely related to the PyVCF package.
I did some digging and this is a known problem with PyVCF: jamescasbon/PyVCF#332

I don't know how to solve this last error since it's possibly related to a defunct package using Python 2.*

To Reproduce

I am able to cleanly install pvactools with mamba, pip and the requirements.txt file from this repo:

mamba create -n pvactools python=3.7.12
mamba activate pvactools
python -m pip install pvactools -r requirements.txt 

Log Output

When I run pvactools I get normal output

usage: pvactools [-h] [-v] {download_cwls} ...

positional arguments:
  {download_cwls}
    download_cwls  Download pVACtools CWLs for each tool's main pipeline

optional arguments:
  -h, --help       show this help message and exit
  -v, --version    Display the currently installed pvactools version (default:
                   False)
Error: No command specified

when I run pvacseq, this happens:

Traceback (most recent call last):
  File "/home/a.vliet/miniconda3/envs/pvactools/bin/pvacseq", line 5, in <module>
    from pvactools.tools.pvacseq.main import main
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/pvactools/tools/pvacseq/__init__.py", line 18, in <module>
    from . import *
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/pvactools/tools/pvacseq/run.py", line 7, in <module>
    from pvactools.lib.prediction_class import *
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/pvactools/lib/__init__.py", line 22, in <module>
    from . import *
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/pvactools/lib/input_file_converter.py", line 1, in <module>
    import vcf
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/vcf/__init__.py", line 9, in <module>
    from vcf.parser import Reader, Writer
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/vcf/parser.py", line 25, in <module>
    from model import _Call, _Record, make_calldata_tuple
ModuleNotFoundError: No module named 'model'

I solved this error by adding lines to __init__.py in the PyVCF package (not ideal).
After solving that error, the one below popped up:

Traceback (most recent call last):
  File "/home/a.vliet/miniconda3/envs/pvactools/bin/pvacseq", line 5, in <module>
    from pvactools.tools.pvacseq.main import main
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/pvactools/tools/pvacseq/__init__.py", line 18, in <module>
    from . import *
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/pvactools/tools/pvacseq/run.py", line 7, in <module>
    from pvactools.lib.prediction_class import *
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/pvactools/lib/__init__.py", line 22, in <module>
    from . import *
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/pvactools/lib/input_file_converter.py", line 1, in <module>
    import vcf
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/vcf/__init__.py", line 9, in <module>
    from vcf.parser import Reader, Writer
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/vcf/parser.py", line 635, in <module>
    class Writer(object):
  File "/home/a.vliet/miniconda3/envs/pvactools/lib/python3.7/site-packages/vcf/parser.py", line 639, in Writer
    counts = dict((v,k) for k,v in field_counts.iteritems())
AttributeError: 'dict' object has no attribute 'iteritems'

[susannasiebert]

That's odd; we haven't run into a problem like this before. We're actually no longer using the pyvcf package so that import can be removed. There are, however, some downstream dependencies using that package so you might still get errors.

[susannasiebert]

I removed the import and made a new release (3.1.1). I'm still working on the docker containers but since you're installing it directly, please try to upgrade to the latest version and see if that fixes the error you're seeing.

[bozbezbozzel]

Thanks so much for your quick reply. Will give it a go tomorrow and let you know what happened. I was surprised I could not find someone who encountered the same problem but I've been breaking my head over it for 2 days.

[bozbezbozzel]

I did

mamba create -n pvactools python=3.7.12
mamba activate pvactools
python -m pip install pvactools==3.1.1 -r requirements.txt 

And that got rid of the error! Thanks so much for your help, Susanna. Happy holidays and happy new year :)