metaLncRNA v2.0.3 🧬🤖

metaLncRNA is a modular, high-performance Python framework designed to identify Long Non-coding RNAs (lncRNAs) by orchestrating an ensemble of seven diverse computational tools. It resolves the "reproducibility gap" by automating environment management and providing a robust consensus prediction through weighted soft-voting.

📂 Repository Structure

.
├── conda/                   # Bioconda recipe and metadata
├── deploy/                  # Containerization (Dockerfile, Singularity.def)
├── docs/                    # Technical documentation and user guides
├── examples/                # Quick-start samples (FASTA, config templates)
├── galaxy/                  # Galaxy Tool wrapper and test data
├── INPI_Registration/       # Legal software registration assets
├── paper/                   # JOSS publication manuscript and bibliography
├── scripts/                 # Bash scripts for HPC/Batch processing
├── src/
│   └── metalncrna/          # Main Python Package
│       ├── cli.py           # Command-line interface entry point
│       ├── adapters/        # Wrappers for 7 lncRNA predictors
│       ├── engine/          # Core logic (Consensus, Dispatcher, Trainer)
│       ├── utils/           # AI Agent, Env management, Reports, FASTA handling
│       ├── data/            # Built-in weights and default configurations
│       └── third_party/     # Bundled legacy tools (CNCI, CPPred, LGC)
├── tests/                   # Comprehensive Unit and Integration tests
├── pyproject.toml           # Build system and dependency definitions
└── pixi.toml                # Environment management configuration

🧩 Core Components Detail

• src/metalncrna/adapters/: Orchestrates external tools like RNAsamba, CPAT, CPC2, etc., providing a unified interface for prediction.
• src/metalncrna/engine/:
  • consensus.py: Implements the weighted soft-voting algorithm.
  • dispatcher.py: Manages parallel execution of the ensemble.
• src/metalncrna/utils/agent.py: Integrates with local LLMs (Ollama) for automated biological interpretation of results.
• galaxy/: Allows metaLncRNA to be integrated into Galaxy instances, supporting reproducible web-based workflows.

🔧 Recent Fixes (v2.0.3)

• 100% Original Sequence ID Preservation: Implemented build_id_mapping and map_df_sequence_ids to ensure original transcript names from transcriptome assemblers (Trinity, StringTie, Cufflinks, etc.) remain intact throughout the entire consensus and reporting pipeline.
• Deduplication & Merge Safety: Prevents Cartesian product row explosions by deduplicating predictions per transcript before cross-tool voting.
• Adapter Attribute Bugfix: Fixed AttributeError caused by missing self.tool_path in BaseAdapter.
• Automatic HTML Dashboard: Integrated HTML report generation directly into metalncrna predict.
• Enhanced AI Agent Feedback: Clear installation guidance and connection diagnostics for Ollama (pip install metalncrna[agent], ollama serve, ollama pull).
• PyPI Release Workflow: Enabled skip-existing: true in GitHub Actions publishing pipeline.

🔧 Previous Fixes (v2.0.0)

• CNCI Stability: Fixed a critical hang in the CNCI legacy tool caused by non-canonical nucleotides (e.g., K, V, M) and a multiprocessing deadlock in the original Python 2.7 implementation.
• Improved Filtering: Implemented rigorous FASTA validation in the CNCI adapter to exclude sequences with ambiguous characters, preventing KeyError crashes.
• Resource Optimization: Optimized tool dispatching by limiting CNCI threads to 4, reducing I/O overhead and improving performance for small-to-medium files.
• Debug Resiliency: The dispatcher now preserves intermediate files automatically if a tool failure occurs, facilitating troubleshooting.

🔧 Previous Fixes (v1.2.1)

• Consensus Logic: Updated consensus_support to reflect the number of tools that agree with the final consensus label, providing better interpretability.
• CPC2 Integration: Fixed a critical parsing error where coding probability and label columns were mismatched (v1.1.8).
• Cleanup: Removed unimplemented/experimental adapters to ensure stability.

⚙️ Configuration

metaLncRNA follows a robust configuration loading order:

1. Internal Defaults: Built-in weights and paths in src/metalncrna/data/default_config.yaml.
2. Local Config: metaLncRNA_config.yaml in your current working directory.
3. User Home: ~/.metalncrna/config.yaml.
4. Explicit Path: Provided via the -c or --config flag.

🚀 Key Features

• Ensemble Prediction: Combines 7 tools (RNAsamba, CPAT, CPC2, PLEK, CNCI, CPPred, LGC).
• Interactive AI Agent: Integrated local LLM assistant (Llama-3.2 or OpenBioLLM) to interpret results and explain classification decisions.
• Reproducibility First: Built-in environment isolation via Mamba and Pixi.
• Standardized Reports: Comprehensive TSV reports with tool congruence metrics.
• Publication Ready: Formatted according to JOSS standards for scientific software.