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' — Reply to this email directly, view it on GitHub <#160 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEEAARAHWOHWLKNG44NIOP3YAPH27AVCNFSM6AAAAAA6J3D3MWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZTG44TQMZTGY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- 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.