ENH: Semantic Type for `fetch-busco-db` output

Sann5 commented 10 months ago

About this repo

q2-types-genomics is a qiime2 plugin that defines semantic types (ST) for other plugins.

What's new

The current PR creates a new ST for the fetch-busco-db action which downloads some data to be used in the evaluate-busco action.
Closes #74

Set up an environment

# For linux: 
# export MY_OS="linux"
# For mac:
export MY_OS="osx" 
wget "https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2023.9-py38-"$MY_OS"-conda.yml"
conda env create -n q2-shotgun --file qiime2-shotgun-2023.9-py38-osx-conda.yml
rm "qiime2-shotgun-2023.9-py38-"$MY_OS"-conda.yml"

Run it locally

First, clone the repo and checkout the PR branch:

conda activate q2-shotgun
conda install -c conda-forge -c bioconda busco=5.6.1
conda remove q2-types-genomics q2-types
pip install git+https://github.com/qiime2/q2-types.git
git clone git@github.com:bokulich-lab/q2-types-genomics.git
cd q2-types-genomics
gh pr checkout <PR_num_here>
pip install -e .

Let's get you some data to play with:

cd wherever_you_want_to_download_the_data_to

busco --download "virus"
cd ..

FYI I can't run busco from the visual code terminal (it can find it), only from i-term.

Test it out!

qiime tools import --input-path wherever_you_want_to_download_the_data_to --output-path busco_db.qza --type "ReferenceDB[BuscoDB]"

Running the tests

pytest -W ignore -vv --pyargs q2_types_genomics

codecov[bot] commented 10 months ago

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (3b993ed) 96.77% compared to head (15615ed) 96.78%.

Files	Patch %	Lines
q2_types_genomics/reference_db/_format.py	95.65%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #75 +/- ## ========================================== + Coverage 96.77% 96.78% +0.01% ========================================== Files 42 42 Lines 1548 1586 +38 ========================================== + Hits 1498 1535 +37 - Misses 50 51 +1 ```

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Sann5 commented 10 months ago

I added some test data with the expected file structure and empty files but its a lot of them. Do you think I should follow another approach for testing the BuscoDatabaseDirFmt @misialq?

bokulich-lab / q2-types-genomics