BiNgoViewer 1.0.0__tar.gz

bingoviewer-1.0.0/BiNgoViewer.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: BiNgoViewer
+Version: 1.0.0
+Summary: BiNgo Genome Viewer — a lightweight browser-based genomics viewer
+Author-email: Billy Ngo <billy.ngo0108@gmail.com>
+License: All rights reserved
+Project-URL: Homepage, https://github.com/billy-ngo/bingo-genome-viewer
+Project-URL: Repository, https://github.com/billy-ngo/bingo-genome-viewer
+Keywords: genomics,genome,viewer,browser,bioinformatics,igv
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: fastapi>=0.111.0
+Requires-Dist: uvicorn[standard]>=0.29.0
+Requires-Dist: biopython>=1.83
+Requires-Dist: pyfaidx>=0.8.1
+Requires-Dist: bamnostic>=1.3
+Requires-Dist: python-multipart>=0.0.9
+
+# BiNgo Genome Viewer
+
+A lightweight, browser-based genomics viewer for visualizing genomes, coverage tracks, read alignments, variants, and annotations. Built as a modern alternative to IGV.
+
+## Supported File Formats
+
+| Type | Formats |
+|------|---------|
+| **Genome** | GenBank (`.gb`, `.gbk`), FASTA (`.fasta`, `.fa`) |
+| **Coverage** | BigWig (`.bw`), WIG (`.wig`), BedGraph (`.bedgraph`, `.bdg`) |
+| **Reads** | BAM (`.bam` + `.bai` index) |
+| **Variants** | VCF (`.vcf`, `.vcf.gz`) |
+| **Annotations** | BED (`.bed`), GFF (`.gff`, `.gff3`), GTF (`.gtf`), GenBank (`.gb`) |
+
+## Quick Start
+
+### Install with pip (recommended)
+
+No Node.js required — the frontend is pre-built and bundled.
+
+```bash
+pip install BiNgoViewer
+bingo
+```
+
+This installs the `bingo` command, starts the server, and opens the viewer in your browser. Options:
+
+```bash
+bingo --port 9000        # use a custom port
+bingo --no-browser       # start without opening the browser
+python -m bingoviewer    # alternative way to launch
+```
+
+### Windows (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+Double-click **`launch.bat`**. On first run it will install dependencies automatically, then open the viewer in your browser.
+
+### macOS (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+Double-click **`BiNgo Genome Viewer.command`** (or run `./launch.sh` from a terminal). On first run it will create a virtual environment and install dependencies, then open the viewer in your browser.
+
+> **Permission denied?** If macOS says the file can't be opened, run this once in Terminal from the project folder:
+> ```bash
+> chmod +x launch.sh "BiNgo Genome Viewer.command"
+> ```
+
+### Linux (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+```bash
+chmod +x launch.sh
+./launch.sh
+```
+
+### Docker
+
+```bash
+cd app
+docker-compose up --build
+```
+
+Then open [http://localhost:8000](http://localhost:8000).
+
+## Usage
+
+1. **Load a genome** — Drag and drop a FASTA or GenBank file into the file loader at the top
+2. **Add tracks** — Drag and drop any supported track files (BAM, BigWig, WIG, VCF, BED, GFF, etc.)
+3. **Navigate** — Click and drag on tracks to pan; scroll wheel to zoom; use the coordinate bar to jump to a region
+4. **Track settings** — Click the gear icon to adjust height, color, scale, and bar width for tracks
+5. **Reorder tracks** — Drag the grip handle (`≡`) on any track label to reorder
+6. **Export** — Click Export to save the current view as SVG or PNG
+7. **Save session** — Click Save Session to store your current workspace; restore it later or export as a JSON file
+
+## Project Structure
+
+```
+├── pyproject.toml              # pip package definition
+├── bingoviewer/                # Installable Python package
+│   ├── cli.py                  # `bingo` CLI entry point
+│   ├── server/                 # FastAPI backend (bundled)
+│   └── frontend_dist/          # Pre-built React frontend
+├── launch.bat                  # Windows launcher (from source)
+├── launch.sh                   # macOS / Linux launcher (from source)
+├── BiNgo Genome Viewer.command # macOS double-click launcher
+└── app/                        # Application source code
+    ├── backend/                # Python (FastAPI) REST API
+    ├── frontend/               # React (Vite) user interface
+    ├── Dockerfile              # Docker build
+    └── docker-compose.yml      # Docker Compose config
+```
+
+## Citation
+
+If you use this software in your research, please cite:
+
+> Ngo, B. (2026). BiNgo Genome Viewer (v1.0.0) [Software].
+
+## License
+
+All rights reserved. Contact the author for licensing inquiries.

bingoviewer-1.0.0/BiNgoViewer.egg-info/SOURCES.txt

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+MANIFEST.in
+README.md
+pyproject.toml
+BiNgoViewer.egg-info/PKG-INFO
+BiNgoViewer.egg-info/SOURCES.txt
+BiNgoViewer.egg-info/dependency_links.txt
+BiNgoViewer.egg-info/entry_points.txt
+BiNgoViewer.egg-info/requires.txt
+BiNgoViewer.egg-info/top_level.txt
+bingoviewer/__init__.py
+bingoviewer/__main__.py
+bingoviewer/cli.py
+bingoviewer/frontend_dist/index.html
+bingoviewer/frontend_dist/assets/index-wC3QoUws.js
+bingoviewer/server/__init__.py
+bingoviewer/server/main.py
+bingoviewer/server/models.py
+bingoviewer/server/state.py
+bingoviewer/server/api/__init__.py
+bingoviewer/server/api/data.py
+bingoviewer/server/api/genome.py
+bingoviewer/server/api/tracks.py
+bingoviewer/server/readers/__init__.py
+bingoviewer/server/readers/annotation_reader.py
+bingoviewer/server/readers/bam_reader.py
+bingoviewer/server/readers/bigwig_reader.py
+bingoviewer/server/readers/genbank_reader.py
+bingoviewer/server/readers/genome_reader.py
+bingoviewer/server/readers/vcf_reader.py

bingoviewer-1.0.0/BiNgoViewer.egg-info/dependency_links.txt

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+

bingoviewer-1.0.0/BiNgoViewer.egg-info/entry_points.txt

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+[console_scripts]
+bingo = bingoviewer.cli:main

bingoviewer-1.0.0/BiNgoViewer.egg-info/requires.txt

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+fastapi>=0.111.0
+uvicorn[standard]>=0.29.0
+biopython>=1.83
+pyfaidx>=0.8.1
+bamnostic>=1.3
+python-multipart>=0.0.9

bingoviewer-1.0.0/BiNgoViewer.egg-info/top_level.txt

@@ -0,0 +1 @@
+bingoviewer

bingoviewer-1.0.0/MANIFEST.in

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+recursive-include bingoviewer/frontend_dist *
+recursive-include bingoviewer/server *.py

bingoviewer-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: BiNgoViewer
+Version: 1.0.0
+Summary: BiNgo Genome Viewer — a lightweight browser-based genomics viewer
+Author-email: Billy Ngo <billy.ngo0108@gmail.com>
+License: All rights reserved
+Project-URL: Homepage, https://github.com/billy-ngo/bingo-genome-viewer
+Project-URL: Repository, https://github.com/billy-ngo/bingo-genome-viewer
+Keywords: genomics,genome,viewer,browser,bioinformatics,igv
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: fastapi>=0.111.0
+Requires-Dist: uvicorn[standard]>=0.29.0
+Requires-Dist: biopython>=1.83
+Requires-Dist: pyfaidx>=0.8.1
+Requires-Dist: bamnostic>=1.3
+Requires-Dist: python-multipart>=0.0.9
+
+# BiNgo Genome Viewer
+
+A lightweight, browser-based genomics viewer for visualizing genomes, coverage tracks, read alignments, variants, and annotations. Built as a modern alternative to IGV.
+
+## Supported File Formats
+
+| Type | Formats |
+|------|---------|
+| **Genome** | GenBank (`.gb`, `.gbk`), FASTA (`.fasta`, `.fa`) |
+| **Coverage** | BigWig (`.bw`), WIG (`.wig`), BedGraph (`.bedgraph`, `.bdg`) |
+| **Reads** | BAM (`.bam` + `.bai` index) |
+| **Variants** | VCF (`.vcf`, `.vcf.gz`) |
+| **Annotations** | BED (`.bed`), GFF (`.gff`, `.gff3`), GTF (`.gtf`), GenBank (`.gb`) |
+
+## Quick Start
+
+### Install with pip (recommended)
+
+No Node.js required — the frontend is pre-built and bundled.
+
+```bash
+pip install BiNgoViewer
+bingo
+```
+
+This installs the `bingo` command, starts the server, and opens the viewer in your browser. Options:
+
+```bash
+bingo --port 9000        # use a custom port
+bingo --no-browser       # start without opening the browser
+python -m bingoviewer    # alternative way to launch
+```
+
+### Windows (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+Double-click **`launch.bat`**. On first run it will install dependencies automatically, then open the viewer in your browser.
+
+### macOS (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+Double-click **`BiNgo Genome Viewer.command`** (or run `./launch.sh` from a terminal). On first run it will create a virtual environment and install dependencies, then open the viewer in your browser.
+
+> **Permission denied?** If macOS says the file can't be opened, run this once in Terminal from the project folder:
+> ```bash
+> chmod +x launch.sh "BiNgo Genome Viewer.command"
+> ```
+
+### Linux (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+```bash
+chmod +x launch.sh
+./launch.sh
+```
+
+### Docker
+
+```bash
+cd app
+docker-compose up --build
+```
+
+Then open [http://localhost:8000](http://localhost:8000).
+
+## Usage
+
+1. **Load a genome** — Drag and drop a FASTA or GenBank file into the file loader at the top
+2. **Add tracks** — Drag and drop any supported track files (BAM, BigWig, WIG, VCF, BED, GFF, etc.)
+3. **Navigate** — Click and drag on tracks to pan; scroll wheel to zoom; use the coordinate bar to jump to a region
+4. **Track settings** — Click the gear icon to adjust height, color, scale, and bar width for tracks
+5. **Reorder tracks** — Drag the grip handle (`≡`) on any track label to reorder
+6. **Export** — Click Export to save the current view as SVG or PNG
+7. **Save session** — Click Save Session to store your current workspace; restore it later or export as a JSON file
+
+## Project Structure
+
+```
+├── pyproject.toml              # pip package definition
+├── bingoviewer/                # Installable Python package
+│   ├── cli.py                  # `bingo` CLI entry point
+│   ├── server/                 # FastAPI backend (bundled)
+│   └── frontend_dist/          # Pre-built React frontend
+├── launch.bat                  # Windows launcher (from source)
+├── launch.sh                   # macOS / Linux launcher (from source)
+├── BiNgo Genome Viewer.command # macOS double-click launcher
+└── app/                        # Application source code
+    ├── backend/                # Python (FastAPI) REST API
+    ├── frontend/               # React (Vite) user interface
+    ├── Dockerfile              # Docker build
+    └── docker-compose.yml      # Docker Compose config
+```
+
+## Citation
+
+If you use this software in your research, please cite:
+
+> Ngo, B. (2026). BiNgo Genome Viewer (v1.0.0) [Software].
+
+## License
+
+All rights reserved. Contact the author for licensing inquiries.

bingoviewer-1.0.0/README.md

@@ -0,0 +1,105 @@
+# BiNgo Genome Viewer
+
+A lightweight, browser-based genomics viewer for visualizing genomes, coverage tracks, read alignments, variants, and annotations. Built as a modern alternative to IGV.
+
+## Supported File Formats
+
+| Type | Formats |
+|------|---------|
+| **Genome** | GenBank (`.gb`, `.gbk`), FASTA (`.fasta`, `.fa`) |
+| **Coverage** | BigWig (`.bw`), WIG (`.wig`), BedGraph (`.bedgraph`, `.bdg`) |
+| **Reads** | BAM (`.bam` + `.bai` index) |
+| **Variants** | VCF (`.vcf`, `.vcf.gz`) |
+| **Annotations** | BED (`.bed`), GFF (`.gff`, `.gff3`), GTF (`.gtf`), GenBank (`.gb`) |
+
+## Quick Start
+
+### Install with pip (recommended)
+
+No Node.js required — the frontend is pre-built and bundled.
+
+```bash
+pip install BiNgoViewer
+bingo
+```
+
+This installs the `bingo` command, starts the server, and opens the viewer in your browser. Options:
+
+```bash
+bingo --port 9000        # use a custom port
+bingo --no-browser       # start without opening the browser
+python -m bingoviewer    # alternative way to launch
+```
+
+### Windows (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+Double-click **`launch.bat`**. On first run it will install dependencies automatically, then open the viewer in your browser.
+
+### macOS (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+Double-click **`BiNgo Genome Viewer.command`** (or run `./launch.sh` from a terminal). On first run it will create a virtual environment and install dependencies, then open the viewer in your browser.
+
+> **Permission denied?** If macOS says the file can't be opened, run this once in Terminal from the project folder:
+> ```bash
+> chmod +x launch.sh "BiNgo Genome Viewer.command"
+> ```
+
+### Linux (from source)
+
+Requires Python 3.10+ and Node.js 18+.
+
+```bash
+chmod +x launch.sh
+./launch.sh
+```
+
+### Docker
+
+```bash
+cd app
+docker-compose up --build
+```
+
+Then open [http://localhost:8000](http://localhost:8000).
+
+## Usage
+
+1. **Load a genome** — Drag and drop a FASTA or GenBank file into the file loader at the top
+2. **Add tracks** — Drag and drop any supported track files (BAM, BigWig, WIG, VCF, BED, GFF, etc.)
+3. **Navigate** — Click and drag on tracks to pan; scroll wheel to zoom; use the coordinate bar to jump to a region
+4. **Track settings** — Click the gear icon to adjust height, color, scale, and bar width for tracks
+5. **Reorder tracks** — Drag the grip handle (`≡`) on any track label to reorder
+6. **Export** — Click Export to save the current view as SVG or PNG
+7. **Save session** — Click Save Session to store your current workspace; restore it later or export as a JSON file
+
+## Project Structure
+
+```
+├── pyproject.toml              # pip package definition
+├── bingoviewer/                # Installable Python package
+│   ├── cli.py                  # `bingo` CLI entry point
+│   ├── server/                 # FastAPI backend (bundled)
+│   └── frontend_dist/          # Pre-built React frontend
+├── launch.bat                  # Windows launcher (from source)
+├── launch.sh                   # macOS / Linux launcher (from source)
+├── BiNgo Genome Viewer.command # macOS double-click launcher
+└── app/                        # Application source code
+    ├── backend/                # Python (FastAPI) REST API
+    ├── frontend/               # React (Vite) user interface
+    ├── Dockerfile              # Docker build
+    └── docker-compose.yml      # Docker Compose config
+```
+
+## Citation
+
+If you use this software in your research, please cite:
+
+> Ngo, B. (2026). BiNgo Genome Viewer (v1.0.0) [Software].
+
+## License
+
+All rights reserved. Contact the author for licensing inquiries.

bingoviewer-1.0.0/bingoviewer/__init__.py

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+"""BiNgo Genome Viewer — a lightweight browser-based genomics viewer."""
+
+__version__ = "1.0.0"

bingoviewer-1.0.0/bingoviewer/__main__.py

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+"""
+Entry point for `python -m bingoviewer` and the `bingo` CLI command.
+
+Starts the FastAPI server, serves the bundled frontend, and opens the browser.
+"""
+
+import sys
+from bingoviewer.cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())

bingoviewer-1.0.0/bingoviewer/cli.py

@@ -0,0 +1,64 @@
+"""
+BiNgo Genome Viewer CLI — launch the viewer from the command line.
+
+Usage:
+    bingo                    # start on default port 8000
+    bingo --port 9000        # start on a custom port
+    bingo --no-browser       # start without opening the browser
+"""
+
+import argparse
+import os
+import sys
+import threading
+import time
+import webbrowser
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="bingo",
+        description="BiNgo Genome Viewer — a lightweight browser-based genomics viewer",
+    )
+    parser.add_argument(
+        "--port", type=int, default=8000,
+        help="Port to run the server on (default: 8000)",
+    )
+    parser.add_argument(
+        "--host", type=str, default="127.0.0.1",
+        help="Host to bind to (default: 127.0.0.1)",
+    )
+    parser.add_argument(
+        "--no-browser", action="store_true",
+        help="Don't automatically open the browser",
+    )
+    args = parser.parse_args()
+
+    # Add the backend source directory to sys.path so bare imports
+    # (e.g. `from state import app_state`, `from readers.bam_reader import ...`)
+    # resolve correctly.
+    backend_dir = os.path.join(os.path.dirname(__file__), "server")
+    sys.path.insert(0, backend_dir)
+
+    # Now import the FastAPI app (triggers backend module loading)
+    from bingoviewer.server.main import app  # noqa: E402
+
+    # Open browser after a short delay
+    if not args.no_browser:
+        url = f"http://{args.host}:{args.port}"
+        if args.host in ("0.0.0.0",):
+            url = f"http://localhost:{args.port}"
+
+        def _open():
+            time.sleep(1.5)
+            webbrowser.open(url)
+
+        threading.Thread(target=_open, daemon=True).start()
+
+    # Run the server
+    import uvicorn
+    print(f"\n  BiNgo Genome Viewer running at http://localhost:{args.port}")
+    print("  Press Ctrl+C to stop.\n")
+    uvicorn.run(app, host=args.host, port=args.port, log_level="warning")
+
+    return 0