dsrnascan 0.3.0__tar.gz

dsrnascan-0.3.0/.github/workflows/ci-simple.yml

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+name: CI Tests
+
+on:
+  push:
+    branches: [ main, master, develop ]
+  pull_request:
+    branches: [ main, master ]
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Test - ${{ matrix.os }} - Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11']
+        include:
+          # Test one version on Windows
+          - os: windows-latest
+            python-version: '3.10'
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build wheel
+    
+    - name: Install einverted (Linux)
+      if: runner.os == 'Linux'
+      run: |
+        # Try to install from conda first (fastest)
+        # Note: This requires conda to be available, which it isn't by default
+        # Alternative: compile from source or download pre-compiled binary
+        echo "Note: einverted binary not available for Linux in this test"
+        echo "In production, users should install EMBOSS via their package manager"
+        # For Ubuntu/Debian: sudo apt-get install emboss
+        # For now, we'll skip the functional test on Linux
+    
+    - name: Build package
+      run: python -m build
+    
+    - name: Install package
+      run: pip install dist/*.whl
+    
+    - name: Test CLI
+      run: |
+        dsrnascan --help
+        dsrnascan --version
+    
+    - name: Run functional test (macOS only for now)
+      if: runner.os == 'macOS'
+      run: |
+        echo ">test" > test.fasta
+        echo "GGGGGGGGGGAAAAAAAAAAAAAACCCCCCCCCC" >> test.fasta
+        dsrnascan test.fasta -w 100 -s 50 --score 15 -c 1
+    
+    - name: Skip functional test (Linux/Windows)
+      if: runner.os != 'macOS'
+      run: |
+        echo "Skipping functional test - einverted binary not available for ${{ runner.os }}"
+        echo "Users should install EMBOSS via their system package manager"
+    
+    - name: Verify output files (macOS only)
+      if: runner.os == 'macOS'
+      shell: python
+      run: |
+        import glob
+        import sys
+        
+        # Check for output directory
+        dirs = glob.glob('dsrnascan_*')
+        if not dirs:
+            print('ERROR: No output directory created')
+            sys.exit(1)
+        
+        print(f'✓ Output directory: {dirs[0]}')
+        
+        # Check for results file
+        results = glob.glob(f'{dirs[0]}/*_merged_results.txt')
+        if not results:
+            print('ERROR: No results file created')
+            sys.exit(1)
+        
+        print(f'✓ Results file: {results[0]}')
+        print('All tests passed!')
+
+  test-direct-install:
+    name: Test Direct Install from GitHub
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+    
+    - name: Install from GitHub
+      run: |
+        pip install git+https://github.com/${{ github.repository }}.git@${{ github.sha }}
+    
+    - name: Test installation
+      run: |
+        dsrnascan --help
+        python -c "import dsrnascan; print('Import successful')"

dsrnascan-0.3.0/.github/workflows/quick-test.yml

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+name: Quick Test
+
+on:
+  push:
+    paths:
+      - 'dsRNAscan.py'
+      - 'setup.py'
+      - 'pyproject.toml'
+      - 'requirements.txt'
+  workflow_dispatch:
+
+jobs:
+  quick-test:
+    name: Quick Install Test
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    
+    - name: Install package
+      run: |
+        pip install .
+    
+    - name: Run smoke test
+      run: |
+        dsrnascan --version
+        dsrnascan --help
+        
+        # Quick functional test
+        echo ">test" > test.fa
+        echo "GGGGGGGGGGAAAAAAAAAAAAAACCCCCCCCCC" >> test.fa
+        dsrnascan test.fa -w 100 -s 50 --score 15 -c 1
+        
+        # Verify output was created
+        ls -la dsrnascan_*/

dsrnascan-0.3.0/.github/workflows/release.yml

@@ -0,0 +1,140 @@
+name: Build and Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential autoconf automake libtool
+      
+      - name: Download EMBOSS
+        run: |
+          wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
+          tar -xzf EMBOSS-6.6.0.tar.gz
+      
+      - name: Apply patch and build
+        run: |
+          cd EMBOSS-6.6.0
+          patch -p1 < ../einverted.patch
+          ./configure --without-x --without-pngdriver
+          cd emboss
+          make einverted
+          cp .libs/einverted ../einverted-linux-x86_64
+      
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: einverted-linux-x86_64
+          path: EMBOSS-6.6.0/einverted-linux-x86_64
+
+  build-macos:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v3
+      
+      - name: Install dependencies
+        run: |
+          brew install autoconf automake libtool
+      
+      - name: Download EMBOSS
+        run: |
+          curl -L -o EMBOSS-6.6.0.tar.gz ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
+          tar -xzf EMBOSS-6.6.0.tar.gz
+      
+      - name: Apply patch and build
+        run: |
+          cd EMBOSS-6.6.0
+          patch -p1 < ../einverted.patch
+          ./configure --without-x --without-pngdriver
+          cd emboss
+          make einverted
+          cp .libs/einverted ../einverted-macos-x86_64
+      
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: einverted-macos-x86_64
+          path: EMBOSS-6.6.0/einverted-macos-x86_64
+
+  build-macos-arm64:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v3
+      
+      - name: Install dependencies
+        run: |
+          brew install autoconf automake libtool
+      
+      - name: Download EMBOSS
+        run: |
+          curl -L -o EMBOSS-6.6.0.tar.gz ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
+          tar -xzf EMBOSS-6.6.0.tar.gz
+      
+      - name: Apply patch and build for ARM64
+        run: |
+          cd EMBOSS-6.6.0
+          patch -p1 < ../einverted.patch
+          # Cross-compile for ARM64
+          ./configure --without-x --without-pngdriver --host=arm64-apple-darwin
+          cd emboss
+          make einverted CFLAGS="-target arm64-apple-darwin"
+          cp .libs/einverted ../einverted-macos-arm64
+      
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: einverted-macos-arm64
+          path: EMBOSS-6.6.0/einverted-macos-arm64
+
+  release:
+    needs: [build-linux, build-macos, build-macos-arm64]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      
+      - name: Download all artifacts
+        uses: actions/download-artifact@v3
+      
+      - name: Create install script
+        run: |
+          cp install.sh install-dsrnascan.sh
+          chmod +x install-dsrnascan.sh
+      
+      - name: Create Release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: |
+            einverted-linux-x86_64/einverted-linux-x86_64
+            einverted-macos-x86_64/einverted-macos-x86_64
+            einverted-macos-arm64/einverted-macos-arm64
+            install-dsrnascan.sh
+            dsRNAscan.py
+          body: |
+            ## Installation
+            
+            ### Quick install (recommended):
+            ```bash
+            curl -L https://github.com/Bass-Lab/dsRNAscan/releases/download/${{ github.ref_name }}/install-dsrnascan.sh | bash
+            ```
+            
+            ### Manual install:
+            1. Download the appropriate einverted binary for your platform
+            2. Download dsRNAscan.py
+            3. Make both executable and add to your PATH
+            
+            ### Supported platforms:
+            - Linux x86_64
+            - macOS x86_64 (Intel)
+            - macOS ARM64 (Apple Silicon)
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

dsrnascan-0.3.0/.gitignore

@@ -0,0 +1,81 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# IDEs
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# dsRNAscan specific
+*.dsRNApredictions.bp
+*_merged_results.txt
+*_ein_results.txt
+test_sequence.fa
+*.test_chr.*
+EMBOSS-6.6.0/
+EMBOSS-6.6.0.tar.gz
+emboss_install/
+
+# Temporary files
+*.tmp
+*.temp
+*.log

dsrnascan-0.3.0/LICENSE

@@ -0,0 +1,21 @@
+GNU GENERAL PUBLIC LICENSE
+Version 3, 29 June 2007
+
+dsRNAscan - A tool for genome-wide prediction of double-stranded RNA structures
+Copyright (C) 2024 Bass Lab
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+For the full GPL-3.0 license text, see:
+https://www.gnu.org/licenses/gpl-3.0.txt

dsrnascan-0.3.0/MANIFEST.in

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+include README.md
+include LICENSE
+include einverted.patch
+include einverted.c
+include compile_patched_einverted.sh
+include compile_minimal_einverted.c
+include requirements.txt
+recursive-include dsrnascan/tools *
+recursive-include tools *
+recursive-include conda-recipe *
+exclude test_sequence.fa
+exclude *.dsRNApredictions.bp
+exclude *_merged_results.txt
+exclude *_ein_results.txt
+global-exclude *.pyc
+global-exclude __pycache__
+global-exclude .DS_Store

dsrnascan-0.3.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: dsrnascan
+Version: 0.3.0
+Summary: A tool for genome-wide prediction of double-stranded RNA structures
+Home-page: https://github.com/Bass-Lab/dsRNAscan
+Author: Bass Lab
+Author-email: 
+License: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/Bass-Lab/dsRNAscan
+Project-URL: Documentation, https://github.com/Bass-Lab/dsRNAscan/blob/main/README.md
+Project-URL: Repository, https://github.com/Bass-Lab/dsRNAscan
+Project-URL: Bug Tracker, https://github.com/Bass-Lab/dsRNAscan/issues
+Keywords: bioinformatics,RNA,dsRNA,secondary structure,genomics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS :: MacOS X
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython>=1.78
+Requires-Dist: numpy>=1.19
+Requires-Dist: pandas>=1.1
+Requires-Dist: ViennaRNA>=2.4
+Provides-Extra: mpi
+Requires-Dist: mpi4py>=3.0; extra == "mpi"
+Requires-Dist: parasail>=1.2; extra == "mpi"
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov>=2.0; extra == "dev"
+Requires-Dist: black>=22.0; extra == "dev"
+Requires-Dist: flake8>=4.0; extra == "dev"
+Requires-Dist: mypy>=0.900; extra == "dev"
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+# dsRNAscan
+
+[![CI Tests](https://github.com/Bass-Lab/dsRNAscan/actions/workflows/ci-simple.yml/badge.svg)](https://github.com/Bass-Lab/dsRNAscan/actions/workflows/ci-simple.yml)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+
+**dsRNAscan** is a bioinformatics tool for genome-wide identification of **double-stranded RNA (dsRNA) structures**. It uses a sliding window approach to detect inverted repeats that can form dsRNA secondary structures, with special support for **G-U wobble base pairing** critical for RNA analysis.
+
+## 🚀 Quick Start
+
+### Install from PyPI (Coming Soon)
+```bash
+pip install dsrnascan
+```
+
+### Install from GitHub  
+```bash
+# Direct from GitHub with automatic einverted compilation
+pip install --no-binary :all: git+https://github.com/Bass-Lab/dsRNAscan.git
+
+# Or if you prefer using pre-built wheels (faster but einverted needs separate setup)
+pip install git+https://github.com/Bass-Lab/dsRNAscan.git
+```
+
+### Install from Local Files
+```bash
+# Option 1: Clone and install with einverted compilation
+git clone https://github.com/Bass-Lab/dsRNAscan.git
+cd dsRNAscan
+pip install --no-binary :all: .
+
+# Option 2: Quick install (uses pre-compiled binaries if available)
+git clone https://github.com/Bass-Lab/dsRNAscan.git
+cd dsRNAscan
+pip install .
+
+# Option 3: Development mode (editable install)
+git clone https://github.com/Bass-Lab/dsRNAscan.git
+cd dsRNAscan
+pip install -e .
+
+# Option 4: Manual einverted compilation then install
+git clone https://github.com/Bass-Lab/dsRNAscan.git
+cd dsRNAscan
+./compile_patched_einverted.sh  # Compile einverted with G-U patch
+pip install .
+```
+
+### Basic Usage
+```bash
+# Scan a genome/sequence for dsRNA structures
+dsrnascan input.fasta -w 10000 -s 150 --score 50
+
+# Process specific chromosome
+dsrnascan genome.fasta --chr chr21 -c 8
+
+# Use custom parameters for sensitive detection
+dsrnascan sequence.fasta -w 5000 --min 20 --score 30
+```
+
+## 📋 Requirements
+
+- **Python 3.8+**
+- **Dependencies** (automatically installed):
+  - numpy ≥1.19
+  - pandas ≥1.1
+  - biopython ≥1.78
+  - ViennaRNA ≥2.4
+
+### Important: einverted Binary
+
+dsRNAscan requires the `einverted` tool from EMBOSS with our **G-U wobble patch** for accurate RNA structure detection. 
+
+**Option 1: Automatic** (macOS with included binary)
+- The package includes a pre-compiled einverted for macOS ARM64
+- It will be used automatically on compatible systems
+
+**Option 2: System Installation** (Linux/Other)
+```bash
+# Ubuntu/Debian
+sudo apt-get install emboss
+
+# macOS with Homebrew
+brew install emboss
+
+# Conda (recommended for bioinformatics workflows)
+conda install -c bioconda emboss
+```
+
+**Note:** System-installed EMBOSS won't have the G-U patch. For full RNA functionality with G-U wobble pairs, compile from source:
+
+```bash
+# Compile with G-U patch (optional but recommended)
+cd dsRNAscan
+DSRNASCAN_COMPILE_FULL=true pip install .
+```
+
+## 🧬 Key Features
+
+- **G-U Wobble Base Pairing**: Modified einverted algorithm specifically for RNA
+- **Parallel Processing**: Multi-CPU support for genome-scale analysis
+- **Flexible Windowing**: Customizable window and step sizes
+- **RNA Structure Prediction**: Integration with ViennaRNA for structure validation
+- **Multiple Output Formats**: Tab-delimited results and IGV visualization files
+
+## 📖 Detailed Usage
+
+### Command-Line Options
+
+```bash
+dsrnascan --help
+```
+
+Key parameters:
+- `-w/--window`: Window size for scanning (default: 10000)
+- `-s/--step`: Step size between windows (default: 150)
+- `--score`: Minimum score threshold for inverted repeats (default: 50)
+- `--min/--max`: Min/max length of inverted repeats (default: 30/10000)
+- `--paired_cutoff`: Minimum percentage of paired bases (default: 70%)
+- `-c/--cpus`: Number of CPUs to use (default: 4)
+- `--chr`: Specific chromosome to process
+- `--reverse`: Scan reverse strand
+
+### Output Files
+
+dsRNAscan generates several output files in a timestamped directory:
+
+1. **`*_merged_results.txt`**: Tab-delimited file with all predicted dsRNAs
+   - Columns include: coordinates, scores, sequences, structures, folding energy
+   
+2. **`*.dsRNApredictions.bp`**: IGV-compatible visualization file
+   - Load in IGV to visualize dsRNA locations on genome
+
+### Example Workflow
+
+```bash
+# 1. Basic genome scan
+dsrnascan human_genome.fa -c 16 --output-dir results/
+
+# 2. Scan specific region with sensitive parameters
+dsrnascan chr21.fa -w 5000 -s 100 --score 30 --min 20
+
+# 3. Process RNA-seq assembled transcripts
+dsrnascan transcripts.fa -w 1000 --paired_cutoff 60
+
+# 4. Scan both strands
+dsrnascan sequence.fa --reverse
+```
+
+## 🔧 Installation Troubleshooting
+
+### "einverted binary not found"
+The package needs einverted from EMBOSS. Solutions:
+1. Install EMBOSS: `conda install -c bioconda emboss`
+2. Or compile during install: `DSRNASCAN_COMPILE_FULL=true pip install .`
+3. Or use the package without functional testing: `dsrnascan --help` works without einverted
+
+### "ModuleNotFoundError: No module named 'ViennaRNA'"
+Install ViennaRNA Python bindings:
+```bash
+# Via conda (recommended)
+conda install -c bioconda viennarna
+
+# Via pip
+pip install ViennaRNA
+```
+
+### Installation on HPC/Cluster
+```bash
+module load python/3.8  # or your Python module
+module load emboss      # if available
+pip install --user git+https://github.com/Bass-Lab/dsRNAscan.git
+```
+
+## 🧪 Testing
+
+Run test with sample data:
+```bash
+# Create test file
+echo ">test_sequence" > test.fasta
+echo "GGGGGGGGGGAAAAAAAAAAAAAACCCCCCCCCC" >> test.fasta
+
+# Run dsRNAscan
+dsrnascan test.fasta -w 100 -s 50 --score 15
+```
+
+## 📚 Algorithm Details
+
+dsRNAscan uses a multi-step approach:
+
+1. **Window Extraction**: Divides genome into overlapping windows
+2. **Inverted Repeat Detection**: Uses modified einverted with G-U wobble support
+3. **Structure Prediction**: Validates structures with RNAduplex (ViennaRNA)
+4. **Filtering**: Applies score and pairing percentage cutoffs
+5. **Parallel Processing**: Distributes windows across multiple CPUs
+
+The key innovation is the **G-U wobble patch** for einverted, allowing detection of RNA-specific base pairs crucial for identifying functional dsRNA structures.
+
+## 📄 Citation
+
+If you use dsRNAscan in your research, please cite:
+```
+Bass Lab. dsRNAscan: A tool for genome-wide prediction of double-stranded RNA structures.
+https://github.com/Bass-Lab/dsRNAscan
+```
+
+## 🤝 Contributing
+
+Contributions are welcome! Please:
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Submit a pull request
+
+## 📝 License
+
+This project is licensed under the GNU General Public License v3.0 - see the [LICENSE](LICENSE) file for details.
+
+## 🆘 Support
+
+- **Issues**: [GitHub Issues](https://github.com/Bass-Lab/dsRNAscan/issues)
+- **Documentation**: [GitHub Wiki](https://github.com/Bass-Lab/dsRNAscan/wiki)
+
+## Acknowledgments
+
+- EMBOSS team for the einverted tool
+- ViennaRNA team for RNA folding algorithms
+- All contributors to the project
+
+---
+**Note**: This tool is for research purposes. Ensure you understand the parameters for your specific use case.