genomix-cli 0.1.0__tar.gz

genomix_cli-0.1.0/.gitignore

@@ -0,0 +1,15 @@
+__pycache__/
+*.pyc
+*.egg-info/
+dist/
+build/
+.genomix/
+.env
+*.bam
+*.bai
+*.vcf.gz
+*.fastq.gz
+.pytest_cache/
+.venv/
+firebase-debug.log
+.DS_Store

genomix_cli-0.1.0/LICENSE

@@ -0,0 +1,194 @@
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genomix_cli-0.1.0/PKG-INFO

@@ -0,0 +1,217 @@
+Metadata-Version: 2.4
+Name: genomix-cli
+Version: 0.1.0
+Summary: AI-powered CLI for DNA sequence and genome analysis
+Author: Genomix Contributors
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: ai,bioinformatics,cli,dna,genomics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: anthropic>=0.40
+Requires-Dist: httpx>=0.27
+Requires-Dist: mcp>=1.0
+Requires-Dist: openai>=1.50
+Requires-Dist: prompt-toolkit>=3.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=13.0
+Description-Content-Type: text/markdown
+
+# Genomix CLI
+
+```
+   ██████╗ ███████╗███╗   ██╗ ██████╗ ███╗   ███╗██╗██╗  ██╗
+  ██╔════╝ ██╔════╝████╗  ██║██╔═══██╗████╗ ████║██║╚██╗██╔╝
+  ██║  ███╗█████╗  ██╔██╗ ██║██║   ██║██╔████╔██║██║ ╚███╔╝
+  ██║   ██║██╔══╝  ██║╚██╗██║██║   ██║██║╚██╔╝██║██║ ██╔██╗
+  ╚██████╔╝███████╗██║ ╚████║╚██████╔╝██║ ╚═╝ ██║██║██╔╝ ██╗
+   ╚═════╝ ╚══════╝╚═╝  ╚═══╝ ╚═════╝ ╚═╝     ╚═╝╚═╝╚═╝  ╚═╝
+```
+
+**AI-powered CLI for DNA sequence and genome analysis.**
+
+<p align="center">
+  <img src="docs/demo.svg" alt="Genomix CLI Demo" width="800">
+</p>
+
+Genomix is an intelligent command-line tool that helps biologists, bioinformaticians, and researchers analyze genomic data through natural language. Ask questions about your VCF, FASTA, or FASTQ files — the AI reads them, queries real databases (NCBI, Ensembl, ClinVar), and explains results in accessible language.
+
+**Local-first.** Runs with Ollama by default — your genomic data never leaves your machine.
+
+## What It Does
+
+```
+❯ Read raw_variants.vcf and give me a clinical summary
+
+  ⚡ read_file(path='raw_variants.vcf')
+    ↳ ##fileformat=VCFv4.2 ...
+
+  1. BRCA1 missense (chr17:43094464): Pathogenic — increased breast/ovarian cancer risk
+  2. CFTR deletion (chr7:117559593): Pathogenic — cystic fibrosis (homozygous)
+  3. HBB missense (chr11:5226773): Pathogenic — sickle cell trait (carrier)
+  4. APOE missense (chr19:44908822): Risk factor — Alzheimer's disease
+  ...
+
+❯ What does this reveal about the person's ancestry?
+
+  Based on the variant profile:
+  - HBB/rs334 (sickle cell trait): high frequency in African/Mediterranean populations
+  - CFTR deltaF508: most common in Northern European populations
+  - Combined profile suggests mixed European/African ancestry
+```
+
+## Features
+
+- **Natural language interface** — ask questions about your genomic data in plain English or French
+- **9 MCP servers** — samtools, BWA, GATK, BLAST+, FastQC, NCBI, Ensembl, ClinVar, dbSNP
+- **Smart analysis** — reads raw VCFs (no annotations needed), identifies genes from coordinates, infers clinical significance
+- **Ancestry inference** — population frequency analysis via gnomAD/1000 Genomes
+- **12 built-in skills** — specialized AI instructions for sequencing, comparative genomics, and exploration workflows
+- **3 AI providers** — Ollama/local (default), Claude (Anthropic), OpenAI
+- **Privacy mode** — automatically active with local models, raw sequences never sent to cloud
+- **Slash commands** — `/qc`, `/align`, `/variant-call`, `/blast`, `/msa`, `/explain`, and more
+- **MCP management** — `/mcp` to view, connect, and manage bioinformatics tool servers
+
+## Installation
+
+```bash
+# Install
+pip install genomix-cli
+
+# Check dependencies
+genomix setup
+
+# Initialize a project
+cd my-analysis/
+genomix init
+```
+
+### Requirements
+
+- Python 3.11+
+- [Ollama](https://ollama.ai) with a model (e.g., `ollama pull qwen3-coder:30b`)
+- Optional: samtools, BWA, GATK, BLAST+ for bioinformatics tools
+
+## Quick Start
+
+```bash
+# Start interactive mode
+genomix
+
+# Non-interactive usage
+genomix ask "What is the BRCA1 gene?"
+genomix ask "Read sample.vcf and summarize the variants"
+genomix run /qc data/reads.fastq.gz
+```
+
+### Interactive Session
+
+```
+   ██████╗ ███████╗███╗   ██╗ ██████╗ ███╗   ███╗██╗██╗  ██╗
+  ...
+  v0.1.0 — AI-powered genome analysis
+
+  ┌──────────────────────────────────────────────────────┐
+  │  Project    BRCA Analysis - Cohort 2026              │
+  │  Organism   Homo sapiens                             │
+  │  Reference  GRCh38                                   │
+  │  Provider   opencode (qwen3-coder:30b)               │
+  │  Privacy    🔒 ON                                    │
+  │  MCP        9 registered (4 connected, 5 missing)    │
+  └──────────────────────────────────────────────────────┘
+
+  Connecting MCP servers...
+  Connecting to ClinVar... ✓ (3 tools)
+  Connecting to dbSNP... ✓ (3 tools)
+  Connecting to Ensembl... ✓ (5 tools)
+  Connecting to NCBI... ✓ (4 tools)
+
+❯ _
+```
+
+## Slash Commands
+
+| Command | Description |
+|---------|-------------|
+| **Analysis** | |
+| `/qc` | Quality control (FastQC) |
+| `/align` | Align reads to reference genome |
+| `/variant-call` | Call variants (GATK/FreeBayes) |
+| `/annotate` | Annotate variants (SnpEff/VEP) |
+| `/pipeline` | Full pipeline: QC → align → call → annotate |
+| **Comparative** | |
+| `/blast` | BLAST similarity search |
+| `/msa` | Multiple sequence alignment |
+| `/phylo` | Phylogenetic tree construction |
+| **Exploration** | |
+| `/summary` | Summarize a genomic file |
+| `/search` | Query databases (NCBI, Ensembl...) |
+| `/explain` | Explain a variant, gene, or region |
+| **Session** | |
+| `/mcp` | Manage MCP servers (connect, status) |
+| `/swarm` | Show background analyses |
+| `/provider` | Switch AI provider |
+| `/model` | Switch model |
+| `/help` | Show available commands |
+
+## Architecture
+
+```
+┌─────────────────────────────────────────────┐
+│              genomix-cli                     │
+│                                              │
+│  CLI/TUI ── Agent Loop ── Swarm Manager      │
+│                 │                             │
+│    ┌────────────┼────────────┐                │
+│    ▼            ▼            ▼                │
+│  Tool       Skills       Project              │
+│  Registry   System       Manager              │
+│    │                                          │
+│    ▼                                          │
+│  MCP Servers                                  │
+│  ├── biotools: samtools, BWA, GATK,           │
+│  │   BLAST+, FastQC                           │
+│  └── databases: NCBI, Ensembl,                │
+│      ClinVar, dbSNP                           │
+│                                               │
+│  AI Providers                                 │
+│  Ollama (local) │ Claude │ OpenAI             │
+└───────────────────────────────────────────────┘
+```
+
+## Configuration
+
+```yaml
+# ~/.genomix/config.yaml
+provider:
+  default: opencode        # ollama local (default)
+  model: qwen3-coder:30b
+
+# Or use Claude/OpenAI:
+# provider:
+#   default: claude
+#   model: claude-sonnet-4-6
+```
+
+API keys (if using cloud providers):
+```yaml
+# ~/.genomix/secrets.yaml (mode 0600)
+anthropic_api_key: "sk-ant-..."
+openai_api_key: "sk-..."
+```
+
+## Contributing
+
+Contributions welcome! This project is in early alpha.
+
+- **Spec:** `docs/superpowers/specs/2026-03-21-genomix-cli-design.md`
+- **Plan:** `docs/superpowers/plans/2026-03-21-genomix-cli.md`
+- **Skills guide:** Create custom skills in `.genomix/skills/` following the SKILL.md format
+
+## License
+
+Apache 2.0

genomix_cli-0.1.0/README.md

@@ -0,0 +1,194 @@
+# Genomix CLI
+
+```
+   ██████╗ ███████╗███╗   ██╗ ██████╗ ███╗   ███╗██╗██╗  ██╗
+  ██╔════╝ ██╔════╝████╗  ██║██╔═══██╗████╗ ████║██║╚██╗██╔╝
+  ██║  ███╗█████╗  ██╔██╗ ██║██║   ██║██╔████╔██║██║ ╚███╔╝
+  ██║   ██║██╔══╝  ██║╚██╗██║██║   ██║██║╚██╔╝██║██║ ██╔██╗
+  ╚██████╔╝███████╗██║ ╚████║╚██████╔╝██║ ╚═╝ ██║██║██╔╝ ██╗
+   ╚═════╝ ╚══════╝╚═╝  ╚═══╝ ╚═════╝ ╚═╝     ╚═╝╚═╝╚═╝  ╚═╝
+```
+
+**AI-powered CLI for DNA sequence and genome analysis.**
+
+<p align="center">
+  <img src="docs/demo.svg" alt="Genomix CLI Demo" width="800">
+</p>
+
+Genomix is an intelligent command-line tool that helps biologists, bioinformaticians, and researchers analyze genomic data through natural language. Ask questions about your VCF, FASTA, or FASTQ files — the AI reads them, queries real databases (NCBI, Ensembl, ClinVar), and explains results in accessible language.
+
+**Local-first.** Runs with Ollama by default — your genomic data never leaves your machine.
+
+## What It Does
+
+```
+❯ Read raw_variants.vcf and give me a clinical summary
+
+  ⚡ read_file(path='raw_variants.vcf')
+    ↳ ##fileformat=VCFv4.2 ...
+
+  1. BRCA1 missense (chr17:43094464): Pathogenic — increased breast/ovarian cancer risk
+  2. CFTR deletion (chr7:117559593): Pathogenic — cystic fibrosis (homozygous)
+  3. HBB missense (chr11:5226773): Pathogenic — sickle cell trait (carrier)
+  4. APOE missense (chr19:44908822): Risk factor — Alzheimer's disease
+  ...
+
+❯ What does this reveal about the person's ancestry?
+
+  Based on the variant profile:
+  - HBB/rs334 (sickle cell trait): high frequency in African/Mediterranean populations
+  - CFTR deltaF508: most common in Northern European populations
+  - Combined profile suggests mixed European/African ancestry
+```
+
+## Features
+
+- **Natural language interface** — ask questions about your genomic data in plain English or French
+- **9 MCP servers** — samtools, BWA, GATK, BLAST+, FastQC, NCBI, Ensembl, ClinVar, dbSNP
+- **Smart analysis** — reads raw VCFs (no annotations needed), identifies genes from coordinates, infers clinical significance
+- **Ancestry inference** — population frequency analysis via gnomAD/1000 Genomes
+- **12 built-in skills** — specialized AI instructions for sequencing, comparative genomics, and exploration workflows
+- **3 AI providers** — Ollama/local (default), Claude (Anthropic), OpenAI
+- **Privacy mode** — automatically active with local models, raw sequences never sent to cloud
+- **Slash commands** — `/qc`, `/align`, `/variant-call`, `/blast`, `/msa`, `/explain`, and more
+- **MCP management** — `/mcp` to view, connect, and manage bioinformatics tool servers
+
+## Installation
+
+```bash
+# Install
+pip install genomix-cli
+
+# Check dependencies
+genomix setup
+
+# Initialize a project
+cd my-analysis/
+genomix init
+```
+
+### Requirements
+
+- Python 3.11+
+- [Ollama](https://ollama.ai) with a model (e.g., `ollama pull qwen3-coder:30b`)
+- Optional: samtools, BWA, GATK, BLAST+ for bioinformatics tools
+
+## Quick Start
+
+```bash
+# Start interactive mode
+genomix
+
+# Non-interactive usage
+genomix ask "What is the BRCA1 gene?"
+genomix ask "Read sample.vcf and summarize the variants"
+genomix run /qc data/reads.fastq.gz
+```
+
+### Interactive Session
+
+```
+   ██████╗ ███████╗███╗   ██╗ ██████╗ ███╗   ███╗██╗██╗  ██╗
+  ...
+  v0.1.0 — AI-powered genome analysis
+
+  ┌──────────────────────────────────────────────────────┐
+  │  Project    BRCA Analysis - Cohort 2026              │
+  │  Organism   Homo sapiens                             │
+  │  Reference  GRCh38                                   │
+  │  Provider   opencode (qwen3-coder:30b)               │
+  │  Privacy    🔒 ON                                    │
+  │  MCP        9 registered (4 connected, 5 missing)    │
+  └──────────────────────────────────────────────────────┘
+
+  Connecting MCP servers...
+  Connecting to ClinVar... ✓ (3 tools)
+  Connecting to dbSNP... ✓ (3 tools)
+  Connecting to Ensembl... ✓ (5 tools)
+  Connecting to NCBI... ✓ (4 tools)
+
+❯ _
+```
+
+## Slash Commands
+
+| Command | Description |
+|---------|-------------|
+| **Analysis** | |
+| `/qc` | Quality control (FastQC) |
+| `/align` | Align reads to reference genome |
+| `/variant-call` | Call variants (GATK/FreeBayes) |
+| `/annotate` | Annotate variants (SnpEff/VEP) |
+| `/pipeline` | Full pipeline: QC → align → call → annotate |
+| **Comparative** | |
+| `/blast` | BLAST similarity search |
+| `/msa` | Multiple sequence alignment |
+| `/phylo` | Phylogenetic tree construction |
+| **Exploration** | |
+| `/summary` | Summarize a genomic file |
+| `/search` | Query databases (NCBI, Ensembl...) |
+| `/explain` | Explain a variant, gene, or region |
+| **Session** | |
+| `/mcp` | Manage MCP servers (connect, status) |
+| `/swarm` | Show background analyses |
+| `/provider` | Switch AI provider |
+| `/model` | Switch model |
+| `/help` | Show available commands |
+
+## Architecture
+
+```
+┌─────────────────────────────────────────────┐
+│              genomix-cli                     │
+│                                              │
+│  CLI/TUI ── Agent Loop ── Swarm Manager      │
+│                 │                             │
+│    ┌────────────┼────────────┐                │
+│    ▼            ▼            ▼                │
+│  Tool       Skills       Project              │
+│  Registry   System       Manager              │
+│    │                                          │
+│    ▼                                          │
+│  MCP Servers                                  │
+│  ├── biotools: samtools, BWA, GATK,           │
+│  │   BLAST+, FastQC                           │
+│  └── databases: NCBI, Ensembl,                │
+│      ClinVar, dbSNP                           │
+│                                               │
+│  AI Providers                                 │
+│  Ollama (local) │ Claude │ OpenAI             │
+└───────────────────────────────────────────────┘
+```
+
+## Configuration
+
+```yaml
+# ~/.genomix/config.yaml
+provider:
+  default: opencode        # ollama local (default)
+  model: qwen3-coder:30b
+
+# Or use Claude/OpenAI:
+# provider:
+#   default: claude
+#   model: claude-sonnet-4-6
+```
+
+API keys (if using cloud providers):
+```yaml
+# ~/.genomix/secrets.yaml (mode 0600)
+anthropic_api_key: "sk-ant-..."
+openai_api_key: "sk-..."
+```
+
+## Contributing
+
+Contributions welcome! This project is in early alpha.
+
+- **Spec:** `docs/superpowers/specs/2026-03-21-genomix-cli-design.md`
+- **Plan:** `docs/superpowers/plans/2026-03-21-genomix-cli.md`
+- **Skills guide:** Create custom skills in `.genomix/skills/` following the SKILL.md format
+
+## License
+
+Apache 2.0

genomix_cli-0.1.0/demo.tape

@@ -0,0 +1,41 @@
+Output demo.gif
+
+Set Shell zsh
+Set FontSize 14
+Set Width 1200
+Set Height 700
+Set Theme "Catppuccin Mocha"
+Set Padding 20
+Set TypingSpeed 50ms
+
+# Setup
+Hide
+Type "source ~/Desktop/genomix/.venv/bin/activate && export PYTHONPATH=~/Desktop/genomix && cd /tmp/genomix_test"
+Enter
+Sleep 1s
+Show
+
+# Launch genomix
+Type "python -m genomix.cli"
+Enter
+Sleep 8s
+
+# Show help
+Type "/help"
+Enter
+Sleep 3s
+
+# Ask about a VCF file
+Type "Read brca_variants.vcf and give me a clinical summary of all variants"
+Enter
+Sleep 20s
+
+# Follow-up question
+Type "Which of these variants are most concerning for cancer risk?"
+Enter
+Sleep 15s
+
+# Exit
+Type "/quit"
+Enter
+Sleep 1s