Get_gene_data() function in abc_atlas_access

Technical
1

Hello,

I’m following the “Accessing 10x RNA-seq gene expression data” tutorial in a Google Colab notebook.

First, I installed the latest version of the library directly from GitHub using this command:

!pip install "abc_atlas_access[notebooks] @ git+[https://github.com/alleninstitute/abc_atlas_access.git](https://github.com/alleninstitute/abc_atlas_access.git)"

When try to import the get_gene_data function as instructed in the tutorial:
>> from abc_atlas_access.abc_atlas_cache.anndata_utils import get_gene_data

I receive the following error:

ModuleNotFoundError: No module named 'abc_atlas_access.abc_atlas_cache.anndata_utils'

It seems this function has been moved or is no longer accessible at this path in the latest version of the library.

2

Hi,

Are you running this code in a notebook, or from a terminal window.

When I run the commands you are running from a terminal window, everything works. I am able to import get_gene_data from the prescribed location.

Is it possible you need to restart your notebook kernel after running the !pip install… command so that the notebook can detect the newly installed software? Are you able to successfully run

import abc_atlas_access

Do you mind providing a link to the notebook you are using, so that I can see exactly what you are seeing?