Can't run FFPolish

[MoyukhShabon]

I followed the instructions for installation, however, the program refuses to run.

$ ffpolish -h
Traceback (most recent call last):
  File "/home/moyukh/miniconda3/envs/ffpolish/bin/ffpolish", line 5, in <module>
    from filter import filter
  File "/home/moyukh/miniconda3/envs/ffpolish/bin/filter.py", line 11, in <module>
    import vaex
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/vaex/__init__.py", line 40, in <module>
    import vaex.dataframe
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/vaex/dataframe.py", line 17, in <module>
    import vaex.utils
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/vaex/utils.py", line 19, in <module>
    import progressbar
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/progressbar/__init__.py", line 5, in <module>
    from .bar import DataTransferBar
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/progressbar/bar.py", line 13, in <module>
    from python_utils import types
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/python_utils/__init__.py", line 1, in <module>
    from . import (
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/python_utils/converters.py", line 89
    if match := regexp.search(input_):
              ^
SyntaxError: invalid syntax

This might be due to a mismatch in the Python package dependency version. But I am not quite sure.

My Conda channels are also prioritized as recommended:

$ conda config --show channels
channels:
  - conda-forge
  - bioconda
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r

Has anyone else run into this issue?

[MingL196]

+1

I am also running into this error.

[MoyukhShabon]

+1

I am also running into this error.

Hi,

I was able to fix this issue and some of the subsequent issues by tweaking the source code. You can find it in my fork of this repo: https://github.com/MoyukhShabon/ffpolish

You can refer to the "Custom Installation Procedure" section of the README for the installation guideline and the "Source Code modifications" section for an overview of the changes made.

Also, my fork does not output a filtered VCF but a table with classification scores. If you need the filtered VCF, you may uncomment the VCF Filtering Block in src/filter.py.

Hope this helps!

[MingL196]

It works!

There was just one extra thing that needed to be added. The software uses an old version of pydantic, so when setting up the conda environment, I needed to specify that pydantic=1.10

i.e.

conda create -n ffpolish -c conda-forge -c bioconda python=3.8 convert_zero_one_based pandas numpy scikit-learn tqdm pysam vaex bam-readcount bedops pydantic=1.10 "python-utils<3.8.0"

Thank you!

[matnguyen]

@MoyukhShabon since I'm not actively maintaining FFPolish anymore, feel free to make a PR! I can generate a new docker container/conda package