Fix predict #116
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| name: Test | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| jobs: | |
| build: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, macos-12, macos-11] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.9.5 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9.5 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Install coreutils (macOS) | |
| if : ${{ matrix.os == 'macos-12' || matrix.os == 'macos-11' }} | |
| run: | | |
| brew update-reset | |
| brew install coreutils | |
| - name: metafx metafast | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx metafast -t 6 -m 6G -k 31 -i test_data/test/* test_data/3* test_data/4* -b1 200 -b2 5000 -l 50 -w wd_metafast --skip-graph | |
| - name: metafx colored | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx colored -t 6 -m 6G -k 31 -i test_data/sample_list_3.txt --n-comps 100 --perc 0.7 -w wd_colored | |
| - name: metafx chisq (with depth) | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx chisq -t 6 -m 6G -k 31 -i test_data/sample_list.txt -w wd_chisq_4 -n 1000 | |
| metafx chisq -t 6 -m 6G -k 31 -i test_data/sample_list_3.txt -w wd_chisq_3 --skip-graph -n 10000 --depth 15 | |
| - name: metafx feature_analysis | |
| run: | | |
| export PATH=bin:$PATH | |
| mkdir reads | |
| ln -s `pwd`/test_data/3* reads/ | |
| ln -s `pwd`/test_data/4* reads/ | |
| ln -s `pwd`/test_data/test/* reads/ | |
| metafx feature_analysis -k 31 -t 6 -m 6G -f wd_chisq_4/ -n A_19 -r reads/ --relab 0.5 -w wd_feat_analysis | |
| - name: metafx stats | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx stats -t 6 -m 6G -k 31 -i test_data/sample_list.txt -w wd_stats --skip-graph | |
| - name: metafx metaspades (macOS) | |
| if : ${{ matrix.os == 'macos-12' || matrix.os == 'macos-11' }} | |
| run: | | |
| curl -L https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Darwin.tar.gz -o SPAdes-3.15.5-Darwin.tar.gz | |
| tar -zxf SPAdes-3.15.5-Darwin.tar.gz | |
| export PATH=bin:$PATH | |
| export PATH=SPAdes-3.15.5-Darwin/bin/:$PATH | |
| metafx metaspades -t 6 -m 6G -k 31 -i test_data/33* -b1 100 -b2 1000 -l 50 -w wd_metaspades --skip-graph | |
| - name: metafx metaspades (Linux) | |
| if : matrix.os == 'ubuntu-20.04' | |
| run: | | |
| wget https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Linux.tar.gz | |
| tar -xzf SPAdes-3.15.5-Linux.tar.gz | |
| export PATH=bin:$PATH | |
| export PATH=SPAdes-3.15.5-Linux/bin/:$PATH | |
| metafx metaspades -t 6 -m 6G -k 31 -i test_data/33* -b1 100 -b2 1000 -l 50 -w wd_metaspades --skip-graph | |
| - name: metafx unique & metafx pca | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx unique -t 6 -m 6G -k 31 -i test_data/sample_list_train.txt -w wd_unique_pca --kmers-dir wd_metafast/kmer-counter-many/kmers | |
| metafx pca -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv --show -w wd_pca | |
| - name: metafx fit (RF & XGB & PyTorch) | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx fit -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_fit_rf | |
| metafx fit -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_fit_xgb -e XGB | |
| metafx fit -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_fit_torch -e Torch | |
| - name: metafx cv | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx cv -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_cv -n 2 --grid -t 6 | |
| - name: metafx calc_features | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx calc_features -t 6 -m 6G -k 31 -i test_data/test_*.fastq.gz -d wd_unique_pca -w wd_calc_features | |
| - name: metafx predict | |
| run: | | |
| export PATH=bin:$PATH | |
| echo -e "test_A\tA\ntest_B\tB\ntest_C\tC\ntest_D\tD\n" > test_labels.tsv | |
| metafx predict -f wd_calc_features/feature_table.tsv --model wd_cv/rf_model_cv.joblib -w wd_predict -i test_labels.tsv | |
| - name: metafx fit_predict | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx fit_predict -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_fit_predict | |
| - name: metafx extract_kmers | |
| run: | | |
| export PATH=bin:$PATH | |
| metafx extract_kmers -t 6 -m 6G -k 31 -i test_data/test/* test_data/3* test_data/4* -w wd_kmers | |
| - name: metafx bandage (macOS) | |
| if : ${{ matrix.os == 'macos-12' || matrix.os == 'macos-11' }} | |
| run: | | |
| mkdir Bandage | |
| cd Bandage | |
| curl -L https://github.com/ctlab/BandageNG/releases/download/continuous/BandageNG-macOS.dmg -o BandageNG | |
| chmod +x BandageNG | |
| cd .. | |
| export PATH=bin:$PATH | |
| export PATH=Bandage/:$PATH | |
| export PATH=SPAdes-3.15.5-Darwin/bin/:$PATH | |
| metafx bandage -w wd_bandage --draw-graph -f wd_unique_pca/ -n 20 | |
| - name: metafx bandage (Linux) | |
| if : matrix.os == 'ubuntu-20.04' | |
| run: | | |
| mkdir Bandage | |
| cd Bandage | |
| wget -O BandageNG https://github.com/ctlab/BandageNG/releases/download/continuous/BandageNG-Linux.AppImage | |
| chmod +x BandageNG | |
| cd .. | |
| export PATH=bin:$PATH | |
| export PATH=Bandage/:$PATH | |
| export PATH=SPAdes-3.15.5-Linux/bin/:$PATH | |
| metafx bandage -w wd_bandage --draw-graph -f wd_unique_pca/ -n 20 |