Hello,
I have the import error as below.
I am trying to annotate ‘FS’ and ‘SOR’ parameters using ‘get_site_info_expr(mt, … , array_sum_agg_fields=[‘SB’])’. However, we can see only ‘FS’ value in the results, without ‘SOR’.
Considering both issues, it seems that sor_from_sb() is not working well now.
Please review this issue. Thank you.
Best,
Jina
Which version of gnomad_methods do you have installed?
python3 -m pip show gnomad
Thanks, Dan. I can get the information from the command you suggested.
Name: gnomad
Version: 0.3.0
I just updated gnomad to v0.4.0 and re-run my code, but unfortunately, I got the same error.
Does this work?
python3 -c 'import gnomad.utils.annotations.sor_from_sb'
Unfortunately, I got an error again.
Traceback (most recent call last): File "<string>", line 1, in <module> ModuleNotFoundError: No module named 'gnomad.utils.annotations.sor_from_sb'; 'gnomad.utils.annotations' is not a package
By the way, python3 -c 'import gnomad.utils.annotations.fs_from_sb'' also has the same error.
But, It works as below in python3 mode.
>>> from gnomad.utils.annotations import (fs_from_sb, get_adj_expr, get_lowqual_expr, bi_allelic_expr)
It does not work as below.
>>> from gnomad.utils.annotations import (fs_from_sb, get_adj_expr, get_lowqual_expr, bi_allelic_expr, sor_from_sb)
Sorry, I think this issue is caused by gnomAD’s documentation. The docs at https://broadinstitute.github.io/gnomad_methods/api_reference/ describe the latest development version of the gnomad package, not what’s currently available on PyPI.
In this case, the sor_from_sb function was added since the last PyPI release. To use it, you could install the package from GitHub (https://github.com/broadinstitute/gnomad_methods).
Hello Nick,
Thank you for explaining this issue. I will try this function by referring to your GitHub.
Best,
Jina