Add docstrings #34
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| # This is a basic workflow to test the software | |
| name: main | |
| on: | |
| push: | |
| branches: [ master, dev ] | |
| pull_request: | |
| branches: [ master, dev ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| repository: boasvdp/extract_genes_ABRicate | |
| path: extract_genes_ABRicate | |
| # - name: conda | |
| # run: | | |
| # cd $GITHUB_WORKSPACE/extract_genes_ABRicate | |
| # conda env create -f env.yaml | |
| - name: enter repo folder | |
| run : | | |
| cd $GITHUB_WORKSPACE/extract_genes_ABRicate | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: env.yaml | |
| mamba-version: "*" | |
| - name: test extract_genes_ABRicate | |
| run: | | |
| echo "CONDA_DEFAULT_ENV: $CONDA_DEFAULT_ENV" | |
| python extract_genes_abricate.py --help | |
| # Test with a path | |
| python extract_genes_abricate.py -a test/input/test.tsv -g test/genomes -o test/out -s .fasta | |
| cmp test/correct/correct_blaCTX-M-15.out test/out/input_blaCTX-M-15.out | |
| cmp test/correct/correct_blaCTX-M-15_2.out test/out/input_blaCTX-M-15_2.out | |
| # Testing without a path | |
| python extract_genes_abricate.py -a test/input/test_nopath.tsv -g test/genomes -o test/out_nopath -s .fasta | |
| cmp test/correct/correct_blaCTX-M-15.out test/out_nopath/input_blaCTX-M-15.out | |
| cmp test/correct/correct_blaCTX-M-15_2.out test/out_nopath/input_blaCTX-M-15_2.out | |
| # Testing on csv | |
| python extract_genes_abricate.py -a test/input/test.csv -g test/genomes -o test/out_csv -s .fasta --csv | |
| cmp test/correct/correct_blaCTX-M-15.out test/out_csv/input_blaCTX-M-15.out | |
| cmp test/correct/correct_blaCTX-M-15_2.out test/out_csv/input_blaCTX-M-15_2.out | |
| # Testing for gene cluster | |
| python extract_genes_abricate.py -a test/input/test.tsv -g test/genomes -o test/out_genecluster -s .fasta --genecluster | |
| cmp test/correct/correct_genecluster.fasta test/out_genecluster/input_ncbi.out | |
| # Testing with flanking sequences | |
| python extract_genes_abricate.py -a test/input/flanking.tsv -g test/genomes -o test/out_flanking_5bp --flanking --flanking-bp 5 | |
| cmp test/correct/correct_flanking_5bp.out test/out_flanking_5bp/flanking_blaCTX-M-15.out | |
| # Testing with flanking sequences which run off the contig end | |
| python extract_genes_abricate.py -a test/input/flanking.tsv -g test/genomes -o test/out_flanking_15bp --flanking --flanking-bp 15 | |
| cmp test/correct/correct_flanking_15bp.out test/out_flanking_15bp/flanking_blaCTX-M-15.out | |
| # Test with empty file | |
| python extract_genes_abricate.py -a test/input/test_empty.tsv -g test/genomes -o test/out_empty | |
| - name: Tests with combined ABRicate files from multiple genomes | |
| run: | | |
| # Normal gene extraction should work for files with multiple genomes | |
| python extract_genes_abricate.py -a test/input/test_multiple.tsv -g test/genomes -o test/out_multiple | |
| cmp test/correct/correct_multiple_strainA_blaCTX-M-15.out test/out_multiple/strainA_blaCTX-M-15.out | |
| cmp test/correct/correct_multiple_strainB_blaCTX-M-15.out test/out_multiple/strainB_blaCTX-M-15.out | |
| # Gene cluster extraction should still fail for files with multiple genomes | |
| ! python extract_genes_abricate.py -a test/input/test_multiple.tsv -g test/genomes -o test/out_multiple_genecluster --genecluster |