Vcf preprocessor script

[diegomd90]

I am a novice when it comes to bioinformatics and coding. I am trying to run the preprocessor.py script but I always get the error

ModuleNotFoundError: No module named 'allel'.

I am aware that there is a problem with the sickit allele library. I have tried to install a working version using the commit as you suggest in requirements.txt but I have no success.

However you mention that "the permanent fix is to transition to sgkit, the successor library of scikit-allel".

How exactly do I do that? Do I have to modify the preprocessor.py script to import sgkit?

[markwoon]

Could you please try updating requirements.txt to use

colorama >= 0.4.6
pandas >= 1.5.1
scikit-allel >= 1.3.7
packaging~=21.3

It looks like scikit-allel has fixed the problem.

Then run pip3 install -r requirements.txt again.

[BinglanLi]

Hi,

I am not sure why I didn't see your latest reply on the GitHub issue. Please consider moving the conversation there.

Your error message suggests that your Python cannot find the install scikit-allel package. Please check where the package is installed and the package library path of your Python.

On Sat, Oct 21, 2023 at 6:54 AM diegomd90 @.***> wrote:

Hello;

Thank you;

That allowed me to instal scikit allel, however pharmcat_vcf_preprocessor.py doesn't run:

traceback (most recent call last): File "/media/dell/data/software/pharmcat-preprocessor-2.8.0/preprocessor/pharmcat_vcf_preprocessor.py", line 10, in import preprocessor File "/media/dell/data/software/pharmcat-preprocessor-2.8.0/preprocessor/preprocessor/ init.py", line 3, in from .preprocess import preprocess, preprocess_multiple_files File "/media/dell/data/software/pharmcat-preprocessor-2.8.0/preprocessor/preprocessor/preprocess.py", line 5, in from . import utilities as util File "/media/dell/data/software/pharmcat-preprocessor-2.8.0/preprocessor/preprocessor/utilities.py", line 21, in import allel ModuleNotFoundError: No module named 'allel'

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-- Binglan Li, PhD (She/Her) Postdoctoral Scholar, PharmGKB, Klein Lab Department of Biomedical Data Sciences Stanford University

[BinglanLi]

Closing due to a lack of response. Please feel free to re-open it if you have any further questions.