fixes to gff3-merge - use id instead of name in replace process #10
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| name: build | |
| on: [push] | |
| jobs: | |
| build1-Calculating-coverage: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.9" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install coveralls coverage codecov wheel | |
| pip install . | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Test with coverage | |
| run: | | |
| coverage run -a ./gff3tool/bin/gff3_QC.py -g example_file/example.gff3 -f example_file/reference.fa -o error.txt | |
| coverage run -a ./gff3tool/bin/gff3_fix.py -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3 | |
| coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt | |
| coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -u2 example_file/u2.txt -r merged_report.txt | |
| coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -r merged_report.txt | |
| coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u2 example_file/u2.txt -r merged_report.txt | |
| coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models_w_replace.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt -noAuto | |
| coverage run -a ./gff3tool/bin/gff3_sort.py -g example_file/example.gff3 -og example-sorted.gff3 | |
| coverage run -a ./gff3tool/bin/gff3_to_fasta.py -g example_file/example.gff3 -f example_file/reference.fa -st all -d simple -o test_sequences | |
| - name: after success | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| coverage report | |
| coveralls --service=github | |
| codecov | |
| build2-Checking-links: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: "3.0" | |
| bundler-cache: true # runs 'bundle install' and caches installed gems automatically | |
| - name: Install dependencies | |
| run: gem install awesome_bot | |
| - name: Checking links | |
| run: awesome_bot --allow-redirect --allow-dupe README.md docs/*.md | |
| build3-Testing-functions: | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-latest', 'windows-latest', 'macos-latest'] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.9" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wheel | |
| pip install --no-cache-dir gff3tool | |
| pip install . | |
| - name: script | |
| run: | | |
| gff3_QC -g example_file/example.gff3 -f example_file/reference.fa -o error.txt | |
| gff3_fix -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3 | |
| gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt | |
| gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -u2 example_file/u2.txt -r merged_report.txt | |
| gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -r merged_report.txt | |
| gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u2 example_file/u2.txt -r merged_report.txt | |
| gff3_merge -g1 example_file/new_models_w_replace.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt -noAuto | |
| gff3_sort -g example_file/example.gff3 -og example-sorted.gff3 | |
| gff3_to_fasta -g example_file/example.gff3 -f example_file/reference.fa -st all -d simple -o test_sequences |