Problems running test data

[sarah-r-hume]

Hi,

I'm having issues running the tool with the test data.

I was following the suggested code in the README.md i.e., I created and activated a conda environment using the environment.yaml file.

mamba env create --name geneext --file environment.yaml
mamba activate geneext

And downloaded the test_data files, along with the geneext.py script. However, when I attempt to run it using the provided code

python geneext.py -g test_data/annotation.gtf -b test_data/alignments.bam -o result.gtf --peak_perc 0

I get the following error:

Traceback (most recent call last):
  File "[...]/geneext_practice/geneext.py", line 5, in <module>
    from geneext.config import read_yaml_config
  File "[...]/geneext_practice/geneext.py", line 5, in <module>
    from geneext.config import read_yaml_config
ModuleNotFoundError: No module named 'geneext.config'; 'geneext' is not a package

I see that the README.md and environment.yaml files were last updated over a year ago, whereas the geneext.py file was update just a couple of months ago. Is there a step missing from the Readme that I am supposed to be doing? Are all the dependencies in the environment.yaml file?

I don't use python very often so there may be something obvious I'm missing, but I would appreciate more explicit instructions.

Thanks in advance!
Sarah

[Lil-Psilocybe]

hi Sarah!

I've been running into this issue to. what worked for me was using the updated environment_full.yaml they provide but also changing my channel_config to flexible vs strict (see [](here https://stackoverflow.com/questions/73733991/problem-while-creating-environment-from-yaml-file-iphop)).

[zolotarovgl]

@sarah-r-hume @Lil-Psilocybe
Apologies for a late reply. Indeed, the solution from @Lil-Psilocybe should work.