ngs-agent 0.2.0__tar.gz

ngs_agent-0.2.0/.github/workflows/publish.yml

@@ -0,0 +1,29 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch: {}
+
+permissions:
+  id-token: write   # required for Trusted Publishing (no stored password)
+  contents: read
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tooling
+        run: python -m pip install --upgrade build
+
+      - name: Build distributions
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

ngs_agent-0.2.0/.github/workflows/pylint.yml

@@ -0,0 +1,23 @@
+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+    - 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 pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint $(git ls-files '*.py')

ngs_agent-0.2.0/.github/workflows/test.yml

@@ -0,0 +1,39 @@
+name: Test
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+
+    steps:
+    - 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 -e ".[dev,llm]"
+
+    - name: Run pytest
+      run: |
+        pytest tests/ -v --tb=short
+
+    - name: Run ruff check
+      run: |
+        ruff check ngs_agent/ agents/
+
+    - name: Run mypy
+      run: |
+        mypy ngs_agent/ --ignore-missing-imports

ngs_agent-0.2.0/.gitignore

@@ -0,0 +1,42 @@
+```
+# Dependencies
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+.pytest_cache/
+.mypy_cache/
+.coverage
+coverage/
+htmlcov/
+
+# Build and distribution artifacts
+build/
+dist/
+*.egg-info/
+*.whl
+*.tar.gz
+*.zip
+
+# Environment files
+.env
+.env.local
+*.env.*
+
+# Logs and temporary files
+*.log
+# This small log is part of the documented demo command.
+!demo_data/sample.log
+*.tmp
+*.swp
+
+# Editors and IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# OS generated files
+.DS_Store
+Thumbs.db
+```

ngs_agent-0.2.0/LICENSE

@@ -0,0 +1,201 @@
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+   Copyright 2026 Muhammad Alyan Ashraf
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ngs_agent-0.2.0/PKG-INFO

@@ -0,0 +1,290 @@
+Metadata-Version: 2.5
+Name: ngs-agent
+Version: 0.2.0
+Summary: Pipeline log watcher, VCF/QC interpreter, and multi-agent debate platform for wet-lab NGS teams
+Project-URL: Homepage, https://github.com/ranaalyan1/NGS-Agent
+Project-URL: Repository, https://github.com/ranaalyan1/NGS-Agent
+Project-URL: Bug Tracker, https://github.com/ranaalyan1/NGS-Agent/issues
+Author-email: Muhammad Alyan Ashraf <ranaaliyan887@gmail.com>
+License: Apache-2.0
+License-File: LICENSE
+Keywords: agentic,bioinformatics,cli,ngs,rna-seq,variant,vcf,wet-lab,wgs
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: click>=8.1.7
+Requires-Dist: httpx>=0.28.1
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: rich>=13.9.4
+Requires-Dist: typing-extensions>=4.12.2
+Provides-Extra: dev
+Requires-Dist: boto3>=1.37.0; extra == 'dev'
+Requires-Dist: mypy>=1.15.0; extra == 'dev'
+Requires-Dist: pytest-cov>=6.0.0; extra == 'dev'
+Requires-Dist: pytest>=8.3.5; extra == 'dev'
+Requires-Dist: ruff>=0.9.9; extra == 'dev'
+Provides-Extra: llm
+Requires-Dist: anthropic>=0.49.0; extra == 'llm'
+Requires-Dist: httpx>=0.28.1; extra == 'llm'
+Requires-Dist: openai>=1.0.0; extra == 'llm'
+Provides-Extra: swarm
+Requires-Dist: boto3>=1.37.0; extra == 'swarm'
+Requires-Dist: orjson>=3.10.15; extra == 'swarm'
+Requires-Dist: pydantic-settings>=2.7.1; extra == 'swarm'
+Requires-Dist: pydantic>=2.10.6; extra == 'swarm'
+Requires-Dist: python-dotenv>=1.0.1; extra == 'swarm'
+Requires-Dist: redis>=5.0.0; extra == 'swarm'
+Requires-Dist: structlog>=24.4.0; extra == 'swarm'
+Requires-Dist: temporalio>=1.8.0; extra == 'swarm'
+Requires-Dist: tenacity>=9.0.0; extra == 'swarm'
+Provides-Extra: tui
+Requires-Dist: prompt-toolkit>=3.0; extra == 'tui'
+Requires-Dist: pyfiglet>=1.0; extra == 'tui'
+Description-Content-Type: text/markdown
+
+# NGS-Agent
+
+Agentic bioinformatics CLI for wet-lab NGS teams. Monitor pipeline logs in real time, parse and interpret VCF and QC outputs, and run three-perspective LLM debates on Variants of Uncertain Significance — all from a single `pip install`.
+
+[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue)](https://www.python.org)
+[![License: Apache 2.0](https://img.shields.io/badge/license-Apache%202.0-green)](LICENSE)
+[![PyPI](https://img.shields.io/badge/pypi-ngs--agent-orange)](https://pypi.org/project/ngs-agent/)
+
+---
+
+## Installation
+
+```bash
+pip install ngs-agent
+```
+
+Core install pulls only `click`, `rich`, and `PyYAML`. 
+
+To use the `debate` command with an LLM:
+
+```bash
+pip install "ngs-agent[llm]"
+```
+
+To run the full Temporal-orchestrated swarm pipeline (RNA-Seq, WGS, WES end-to-end):
+
+```bash
+pip install "ngs-agent[swarm]"
+```
+
+---
+
+## Usage
+
+```bash
+ngsagent watch pipeline.log
+ngsagent watch --tail pipeline.log
+ngsagent analyze variants.vcf
+ngsagent analyze variants.vcf --qc multiqc_summary.txt
+ngsagent debate variants.vcf
+ngsagent debate variants.vcf --gene BRCA2
+ngsagent config wizard
+```
+
+Try it immediately with the bundled demo files:
+
+```bash
+ngsagent watch demo_data/sample.log
+ngsagent analyze demo_data/sample.vcf
+```
+
+---
+
+## Commands
+
+### watch
+
+Scans a pipeline log against five built-in failure signatures. Pass `--tail` to follow a log as it grows.
+
+```bash
+ngsagent watch <logfile> [--tail] [--signatures <dir>]
+```
+
+Each match prints the matched line, a plain-English explanation of the failure mode, and a concrete suggested fix. Signature severity levels are `critical` and `warning`. No LLM is involved.
+
+Built-in signatures:
+
+| Name | Severity | Fires when |
+|---|---|---|
+| Adapter Contamination | critical | Adapter sequence detected as overrepresented in reads |
+| Low Alignment Rate | critical | Overall mapping rate below 80% |
+| Low Mean Coverage | critical | Mean sequencing depth below 20x |
+| High PCR Duplication | warning | Duplication rate above 30% |
+| Poor Insert Size | warning | Median insert size below 150 bp |
+
+You can supply your own YAML signatures directory with `--signatures`. The schema is the same as the built-in files under `ngs_agent/signatures/`.
+
+---
+
+### analyze
+
+Parses a VCF file and renders a colour-coded variant report in the terminal. Accepts an optional QC summary text file (MultiQC output or any plaintext file containing metrics).
+
+```bash
+ngsagent analyze <vcffile> [--qc <qcfile>]
+```
+
+VCF parsing reads `GENE`, `CSQ`, `CLNSIG`, and `AF` from the INFO field, and `DP` and `AD` from the sample column to compute read depth and variant allele fraction. Variants are classified automatically:
+
+`Pathogenic` — ClinVar `CLNSIG` contains "pathogenic" without "conflicting"  
+`VUS` — ClinVar `CLNSIG` contains "uncertain", "vus", or "unknown significance"  
+`Other` — everything else (benign, synonymous, unannotated)
+
+QC parsing extracts mapping rate, mean coverage, duplication rate, and Q30 fraction using regex against the file text and grades each metric pass / warn / fail.
+
+---
+
+### debate
+
+Submits every VUS in a VCF to three independent LLM personas simultaneously. Each persona evaluates the variant from a different disciplinary angle, then the tool builds a consensus and recommendation.
+
+```bash
+ngsagent debate <vcffile> [--gene <GENE_SYMBOL>]
+```
+
+The three personas:
+
+`Population Geneticist` — evaluates allele frequency, gnomAD population context, and stratification  
+`Clinical Geneticist` — evaluates ClinVar classification, ACMG criteria, and phenotype fit  
+`Functional Geneticist` — evaluates predicted consequence, splice site impact, and protein-level effect
+
+Consensus logic: if all three agree the variant is pathogenic, it's escalated for clinical follow-up. If all three call it benign, it's flagged for deprioritisation. Mixed opinions surface the disagreement verbatim so the reviewing scientist sees exactly where uncertainty lies.
+
+Requires an LLM backend. Configure one with `ngsagent config wizard`.
+
+---
+
+### config
+
+Manages `~/.ngsagent/config.yaml`.
+
+```bash
+ngsagent config wizard
+ngsagent config show
+ngsagent config set llm anthropic
+ngsagent config set anthropic_model claude-sonnet-4-20250514
+ngsagent config set llm ollama
+ngsagent config set ollama_model llama3.2
+ngsagent config set ollama_host http://localhost:11434
+```
+
+---
+
+## LLM Setup
+
+### Anthropic
+
+```bash
+pip install "ngs-agent[llm]"
+export ANTHROPIC_API_KEY=sk-ant-...
+ngsagent config set llm anthropic
+```
+
+Default model is `claude-sonnet-4-20250514`. Override with `ngsagent config set anthropic_model <model>`.
+
+### Ollama (local, no API key)
+
+```bash
+pip install "ngs-agent[llm]"
+ollama pull llama3.2
+ngsagent config set llm ollama
+```
+
+Ollama talks to `http://localhost:11434` by default. Override the host and model via `config set`.
+
+`watch` and `analyze` always work with no LLM configured. Only `debate` requires one.
+
+---
+
+## Swarm Pipeline (full RNA-Seq / WGS / WES)
+
+NGS-Agent also ships a Temporal-orchestrated Docker swarm that runs complete genomics pipelines end to end. Each bioinformatics tool runs in its own container as an autonomous agent. Claude is embedded at decision points — QC verdict, trim parameter selection, alignment failure diagnosis, and biological interpretation — with deterministic heuristic fallbacks when no API key is set.
+
+**Requirements:** Docker Engine, Python 3.11+, Linux or macOS (WSL2 on Windows)
+
+**Setup:**
+
+```bash
+cp .env.example .env
+pip install "ngs-agent[swarm]"
+docker compose up -d
+bash scripts/build-agents.sh
+python worker.py
+```
+
+**Submit a paired-end RNA-Seq run:**
+
+```bash
+python cli.py submit \
+  --experiment RNA-Seq \
+  --organism human \
+  --ref-genome data/ref/grch38_idx \
+  --gtf data/ref/genes.gtf \
+  --fastq-r1 data/fastq/R1.fastq.gz \
+  --fastq-r2 data/fastq/R2.fastq.gz \
+  --paired
+```
+
+**Check run status:**
+
+```bash
+python cli.py status <run-id>
+```
+
+**RNA-Seq pipeline stages:**
+
+Ingest (read count + paired/single detection) → QC (real FastQC + Claude verdict) → AI Decider (Trimmomatic parameters from Claude) → Trim (conditional) → Align (HISAT2 + samtools, with AI-guided re-trim retry on low mapping rate) → Count (featureCounts) → Differential Expression (DESeq2, PCA, MA plot, volcano, heatmap) → GO Enrichment (clusterProfiler + Claude biological narrative) → Report Builder (self-contained HTML) → Report Agent (OpenRouter narrative summary)
+
+**WGS / WES pipeline stages:**
+
+Ingest → QC → AI Decider → Trim → BWA-MEM2 (with per-region coverage from panel BED) → GATK (MarkDuplicatesSpark → BQSR → HaplotypeCaller) → Annotation (snpEff, variant CSV) → Coverage Gate (halts run if mean depth below threshold) → Report Builder → Report Agent
+
+All file artifacts are uploaded to MinIO at `s3://ngs-artifacts/<run_id>/<agent>/`. Results are content-addressed using blake2b hashes of the inputs, so identical re-runs return from cache instantly without re-executing any container.
+
+---
+
+## Project Layout
+
+```
+ngs_agent/              pip-installable CLI (watch, analyze, debate, config)
+  backends/             LLM provider abstraction: Anthropic, Ollama, NoBackend
+  signatures/           YAML failure signatures loaded by the watch command
+agents/                 Docker containers, one per pipeline step
+  base/base_agent.py    Agent contract: reads AGENT_INPUTS + ROUTING_CONTEXT env vars, prints JSON to stdout
+workflows/              Temporal workflow definitions and activity dispatcher
+shared/                 AgentResult model, MinIO storage helper, Redis+MinIO cache
+cli.py                  Swarm pipeline CLI (submit, status, wizard)
+worker.py               Temporal worker process
+demo_data/              sample.log and sample.vcf for testing without real data
+```
+
+---
+
+## Development
+
+```bash
+git clone https://github.com/ranaalyan1/NGS-Agent.git
+cd NGS-Agent
+pip install -e ".[dev,llm]"
+pytest
+ruff check ngs_agent/
+mypy ngs_agent/
+```
+
+---
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE).