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Merge pull request #195 from GoekeLab/add_ci
add ci
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| @@ -0,0 +1,41 @@ | ||
| name: run-test | ||
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| on: | ||
| push: | ||
| branches: [dev, master] | ||
| pull_request: | ||
| branches: [dev, master] | ||
|
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| # Allows you to run this workflow manually from the Actions tab | ||
| workflow_dispatch: | ||
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| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.8"] | ||
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||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Setup Python # Set Python version | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| # Install pip and pytest | ||
| - name: Install dependencies | ||
| run: | | ||
| pip install . | ||
| - name: Install xpore-package | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install pytest pytest-dependency | ||
| - name: Test with pytest | ||
| run: pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml | ||
| - name: Upload pytest test results | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: pytest-results-${{ matrix.python-version }} | ||
| path: junit/test-results-${{ matrix.python-version }}.xml | ||
| # Use always() to always run this step to publish test results when there are test failures | ||
| if: ${{ always() }} |
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|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| notes: Pairwise comparison without replicates with default parameter setting. | ||
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| data: | ||
| KO: | ||
| rep1: data/data/HEK293T-METTL3-KO-rep1/dataprep | ||
| WT: | ||
| rep1: data/data/HEK293T-WT-rep1/dataprep | ||
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| out: ./out | ||
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| method: | ||
| prefiltering: | ||
| method: t-test | ||
| threshold: 0.1 | ||
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xpore/test/data/data/HEK293T-METTL3-KO-rep1/dataprep/data.index
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|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| idx,start,end | ||
| ENSG00000114125,0,743597 | ||
| ENSG00000159111,743597,1675247 |
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xpore/test/data/data/HEK293T-METTL3-KO-rep1/dataprep/data.json
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xpore/test/data/data/HEK293T-METTL3-KO-rep1/dataprep/data.readcount
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| idx,n_reads | ||
| ENSG00000114125,178 | ||
| ENSG00000159111,125 |
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xpore/test/data/data/HEK293T-METTL3-KO-rep1/dataprep/eventalign.index
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,308 @@ | ||
| transcript_id,read_index,pos_start,pos_end | ||
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| ENST00000393000.3,287,68235986,68421082 | ||
| ENST00000393000.3,286,68421082,68631379 | ||
| ENST00000393000.3,291,68631379,68685085 | ||
| ENST00000393000.3,289,68685085,68840693 | ||
| ENST00000393000.3,290,68840693,69021852 | ||
| ENST00000393000.3,292,69021852,69169927 | ||
| ENST00000393000.3,293,69169927,69287965 | ||
| ENST00000393000.3,294,69287965,69428021 | ||
| ENST00000393000.3,296,69428021,69525874 | ||
| ENST00000393000.3,295,69525874,69670799 | ||
| ENST00000477012.5,297,69670799,69850210 | ||
| ENST00000477012.5,298,69850210,70080527 | ||
| ENST00000477012.5,299,70080527,70295161 | ||
| ENST00000477012.5,300,70295161,70511390 | ||
| ENST00000477012.5,301,70511390,70737029 | ||
| ENST00000477012.5,302,70737029,70958007 | ||
| ENST00000477012.5,304,70958007,71126342 | ||
| ENST00000477012.5,303,71126342,71350795 | ||
| ENST00000463740.5,305,71350795,71536755 | ||
| ENST00000229379.2,306,71536755,71820034 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| idx,start,end | ||
| ENSG00000114125,0,385701 | ||
| ENSG00000159111,385701,929888 | ||
| ENSG00000095380,929888,952343 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| idx,n_reads | ||
| ENSG00000114125,91 | ||
| ENSG00000159111,71 | ||
| ENSG00000095380,1 |
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