Data folder doesn't contain gencode_map_v37.tsv about focus

[SToikumo]

Having the same issue as well.

Please, do indicate if and when you resolve the issue.

Cheers,
Sylvanus

[quattro]

Hi all, can you pull from the latest github and install using setup.py, rather than pip? I believe this was fixed in a recent patch, but not yet pushed to pypi.

[psvkmr]

Hi, I specified --locations grch37.eur.loci.bed, which is the bed file found in pyfocus/data/ld_blocks/ in this repo, and that solved the error for me
Cheers,
Prasanth

[emiuga]

Hi @Penstrep , I wonder what other parameter/settings did you use?
I pointed to the grch37.eur.loci.bed file as you mention, but it did the same as specifying '37:EUR'.
Meaning still got same error. I think the encode_map_v37.tsv file is needed for something else.
Looks like this for me: No such file or directory: '~/.local/lib/python3.10/site-packages/pyfocus/data/gencode_map_v37.tsv'
Of note, I tried to re-install repo from git and setup.py install.
Best,
Emilio

[quattro]

Thanks Emilio, I'll pass this along to lead dev

[emiuga]

Great, hope it can be solved soon. Of note, I also tried with latest version 0.801.
Needless to say, thanks for sharing your work!

[zeyunlu]

@quattro @bhuwankhatri11 @Penstrep @emiuga @SToikumo

Hello everyone,

Thanks for trying MA-FOCUS and bringing this issue to our sight.

We have pushed our newest version v0.802 to pypi and github. Please reinstall our program to see if it can solve the problem. If pip install pyfocus --user doesn't work, please try python setup.py install after cloning the github page.

We also uploaded GWAS summary data to our website for you to test. We will push the 1000G phase 3 LD plink data of EUR and AFR to our website in the near future. If you don't want to wait, feel free to shoot me an email ([email protected]).

Please let me know if you have any questions, and we appreciate any feedback.

Best,
Zeyun

[emiuga]

Dear @zeyunlu
Thanks a lot for the update! is working now.
I did: pip install pyfocus==0.802 --user
All the best,
Emilio