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ENH: Added annotation_dict to AMRFinderPlusAnnotationsDirFmt #7

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merged 4 commits into from
Oct 11, 2024

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VinzentRisch
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@VinzentRisch VinzentRisch commented Oct 11, 2024

solves #8

  • Adds annotation_dict to AMRFinderPlusAnnotationsDirFmt
  • Works similar to the genome_dict of GenomeDataDirectoryFormat in q2-types

Set up an environment

mamba create -y -n q2-amrfinderplus -c https://packages.qiime2.org/qiime2/2024.10/metagenome/staged/ -c conda-forge -c bioconda --strict-channel-priority qiime2 q2-types q2-feature-table q2cli q2-metadata ncbi-amrfinderplus

Run it locally

  1. First, clone the repo and checkout the PR branch:
git clone https://github.com/bokulich-lab/q2-amrfinderplus.git
cd q2-amrfinderplus
git fetch origin pull/7/head:pr-7
git checkout pr-7
pip install -e .

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@misialq misialq left a comment

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Hey @VinzentRisch, looks good - see the small suggestion below: feel free to merge after you address that one.

@annotations.set_path_maker
def annotations_path_maker(self, name, id, dir_name=""):
return os.path.join(dir_name, f"{id}_amr_{name}.tsv")


def _create_path(path, relative, dir_format):
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A docstring here would be nice 🙏

@VinzentRisch VinzentRisch merged commit 095e7d6 into bokulich-lab:main Oct 11, 2024
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2 participants