splicecraft 0.2.0__py3-none-any.whl

splicecraft-0.2.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: splicecraft
+Version: 0.2.0
+Summary: Terminal-based circular plasmid map viewer, sequence editor, and Primer3/Golden Braid primer design workbench
+Project-URL: Homepage, https://github.com/Binomica-Labs/SpliceCraft
+Project-URL: Repository, https://github.com/Binomica-Labs/SpliceCraft
+Project-URL: Issues, https://github.com/Binomica-Labs/SpliceCraft/issues
+Project-URL: Changelog, https://github.com/Binomica-Labs/SpliceCraft/blob/master/CHANGELOG.md
+Author: Binomica Labs
+License: MIT License
+        
+        Copyright (c) 2026 Binomica Labs
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Keywords: bioinformatics,cloning,genbank,golden-braid,molecular-biology,plasmid,primer3,terminal,tui
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Terminals
+Requires-Python: >=3.10
+Requires-Dist: biopython>=1.87
+Requires-Dist: platformdirs>=4.2
+Requires-Dist: primer3-py>=2.3.0
+Requires-Dist: textual>=8.2.3
+Provides-Extra: dev
+Requires-Dist: build; extra == 'dev'
+Requires-Dist: pytest-asyncio>=1.3; extra == 'dev'
+Requires-Dist: pytest>=9.0; extra == 'dev'
+Requires-Dist: twine; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# SpliceCraft
+
+```
+╔═══════════════════════════════════════════════════════════════════════════════╗
+║ ⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶ ║
+║                                                                               ║
+║  ________       __________           _________             ____________       ║
+║  __  ___/__________  /__(_)____________  ____/____________ ___  __/_  /_      ║
+║  _____ \___  __ \_  /__  /_  ___/  _ \  /    __  ___/  __ `/_  /_ _  __/      ║
+║  ____/ /__  /_/ /  / _  / / /__ /  __/ /___  _  /   / /_/ /_  __/ / /_        ║
+║  /____/ _  .___//_/  /_/  \___/ \___/\____/  /_/    \__,_/ /_/    \__/        ║
+║         /_/                                                                   ║
+║                                                                               ║
+║        ·  I n - T e r m i n a l   P l a s m i d   W o r k b e n c h  ·        ║
+║                                                                               ║
+║ ⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶⠶ ║
+╚═══════════════════════════════════════════════════════════════════════════════╝
+```
+
+![SpliceCraft screenshot](https://raw.githubusercontent.com/Binomica-Labs/SpliceCraft/master/screenshot.jpg)
+
+A terminal-based circular plasmid map viewer, sequence editor, **primer design
+workbench**, and **Golden Braid parts domesticator** — rendered entirely in your
+shell. Fetch any GenBank record by accession, load local files, annotate features
+with pLannotate, design diagnostic / cloning / Golden Braid primers with Primer3,
+and edit sequences — without ever leaving the terminal.
+
+---
+
+## Features
+
+### Core visualization & editing
+- **Braille dot-matrix circular map** — plasmids rendered as crisp Unicode braille
+  rings with per-strand feature arcs, directional arrowheads, and proximity-placed
+  labels
+- **Linear map view** — toggle with `v` for a horizontal strip layout
+- **Dithered sequence panel** — per-base DNA viewer with feature bars, restriction
+  site overlays, and double-stranded display
+- **Live NCBI fetch** — pull any GenBank record by accession number on demand
+- **Local file support** — open `.gb` / `.gbk` files directly from disk
+- **Free rotation** — spin the origin left or right with `[` / `]`
+- **Restriction enzyme overlay** — 200+ NEB enzymes including Type IIS
+  (BsaI, BsmBI, BbsI, SapI) with visible recognition arcs + cut markers
+
+### Libraries (all persist to JSON)
+- **Plasmid library** — SnapGene-style collection, auto-saves on import, survives
+  restarts, supports rename and handslip-protected delete
+- **Parts Bin** — Golden Braid L0 parts catalog with user-domesticated parts
+  including sequences and primer pairs
+- **Primer library** — all designed primers with Tm, length, date, status
+  (Designed / Ordered / Validated), multi-select for batch operations
+
+### Primer design (Primer3)
+- **Detection primers** — diagnostic PCR; Primer3 picks the ideal pair within
+  a selected region, 450-550 bp product by default (configurable)
+- **Cloning primers** — RE-site tails + GCGC padding; 30+ common enzymes or
+  type a custom recognition sequence
+- **Golden Braid primers** — BsaI domestication for all L0 positions
+  (Promoter, 5' UTR, CDS, CDS-NS, C-tag, Terminator)
+- **Generic primers** — simple binding primers, no tails
+- Primers can be added to the plasmid map as `primer_bind` features
+- Scrollable `TextArea` for custom sequence input; highlighted text = target
+
+### Annotation
+- **pLannotate integration** — press `Shift+A` (or use the `◈` library button)
+  to auto-annotate a plasmid against pLannotate's curated feature database.
+  Optional — see install notes below
+
+### Feature operations
+- **Feature sidebar** — click a row to highlight on map; click the map to
+  select the feature under the cursor
+- **Undo/redo** — 50-deep snapshot stack for all sequence edits
+- **Delete protection** — focus-aware Delete key; confirmation modal (default
+  focus = No) for library entries
+- **Clipboard** — OSC-52 copy works in Windows Terminal, iTerm2, modern WSL
+
+### Data safety
+- **Atomic saves** — all JSON files written via tempfile + `os.replace`
+- **Automatic backups** — every save writes `*.json.bak` before overwriting
+- **Corrupt-file recovery** — missing files don't crash; corrupt files auto-
+  restore from `.bak` with a warning notification on startup
+
+---
+
+## Installation
+
+Requires **Python 3.10+**.
+
+### From PyPI (recommended)
+
+```bash
+pip install splicecraft
+splicecraft              # empty canvas
+splicecraft L09137       # fetch pUC19 from NCBI
+splicecraft myplasmid.gb # open a local GenBank file
+```
+
+All required dependencies (`textual`, `biopython`, `primer3-py`, `platformdirs`)
+are pulled in automatically. User data (library, parts bin, primers) lives in
+the platform-appropriate data directory:
+
+  | Platform | Path |
+  |---|---|
+  | Linux   | `~/.local/share/splicecraft/` |
+  | macOS   | `~/Library/Application Support/splicecraft/` |
+  | Windows | `%APPDATA%\splicecraft\` |
+
+Override with `SPLICECRAFT_DATA_DIR=/path/to/dir splicecraft`.
+
+### From source
+
+```bash
+git clone https://github.com/Binomica-Labs/SpliceCraft.git
+cd SpliceCraft
+pip install -e .
+```
+
+### Optional dependencies
+
+**pLannotate** (for automatic plasmid annotation via `Shift+A`) — requires conda:
+
+```bash
+conda create -n plannotate -c conda-forge -c bioconda plannotate
+conda activate plannotate
+plannotate setupdb          # one-time ~500 MB BLAST database download
+# then run SpliceCraft from the same conda env
+```
+
+SpliceCraft runs fine without pLannotate — the annotation feature just
+notifies the user how to install it if pressed.
+
+---
+
+## Usage
+
+```bash
+# After pip install:
+splicecraft              # empty canvas
+splicecraft L09137       # fetch pUC19 from NCBI on launch
+splicecraft myplasmid.gb # open a local GenBank file
+splicecraft --version    # print version
+splicecraft --help       # quick usage hint
+```
+
+If running from a git clone (`pip install -e .`), the same commands work;
+you can also still run `python3 splicecraft.py` directly.
+
+---
+
+## Key Bindings
+
+### Main screen
+
+| Key            | Description                            |
+|----------------|----------------------------------------|
+| `[` / `]`      | Rotate map origin left / right         |
+| `Shift+[/]`    | Rotate coarse (10× step)               |
+| `Home`         | Reset origin to 0                      |
+| `,` / `.`      | Circular map aspect wider / taller     |
+| `v`            | Toggle circular ↔ linear map           |
+| `l`            | Toggle feature label connector lines   |
+| `r`            | Toggle restriction-site overlay        |
+| `f`            | Fetch a record from NCBI by accession  |
+| `o`            | Open a `.gb` file from disk            |
+| `a`            | Add current plasmid to the library     |
+| `Shift+A`      | Annotate plasmid with pLannotate       |
+| `Shift+E`      | Enter sequence editor mode             |
+| `Shift+S`      | Save edits to file                     |
+| `Delete`       | Context-aware delete (feature or library entry) |
+| `Ctrl+Z`       | Undo                                   |
+| `Ctrl+Shift+Z` | Redo                                   |
+| `Ctrl+C`       | Copy selection to clipboard            |
+| `q`            | Quit                                   |
+
+### Primer Design screen
+
+| Key   | Description                                    |
+|-------|------------------------------------------------|
+| `esc` | Close primer screen                            |
+| `m`   | Mark / unmark primer under cursor (`★`)        |
+| `M`   | Mark / unmark all primers                      |
+| `S`   | Cycle status: Designed → Ordered → Validated   |
+| `Tab` | Cycle focus between fields                     |
+
+### Mouse
+
+| Action         | Description                                 |
+|----------------|---------------------------------------------|
+| Click          | Place cursor / select feature under pointer |
+| Double-click   | Select full feature span                    |
+| Drag           | Select a sequence range                     |
+| Scroll wheel   | Rotate map (when over map panel)            |
+
+---
+
+## Menus
+
+| Menu       | Items                                                              |
+|------------|--------------------------------------------------------------------|
+| File       | Open .gb file · Fetch from NCBI · Add to Library · Save · Quit     |
+| Edit       | Edit Sequence · Undo · Redo · Delete Feature                       |
+| Enzymes    | Show RE sites · Unique cutters · 6+/4+ bp sites · Connectors       |
+| Features   | Add Feature · Delete Feature · Annotate with pLannotate            |
+| Primers    | Opens the full-screen Primer Design workbench                      |
+| Parts      | Opens the Parts Bin (Golden Braid L0 parts catalog)                |
+| Constructor| Opens the Assembly Constructor for TU building                     |
+
+---
+
+## Requirements
+
+| Package           | Version           | Purpose                                      |
+|-------------------|-------------------|----------------------------------------------|
+| Python            | ≥ 3.10            | Runtime                                      |
+| Textual           | ≥ 8.2.3           | TUI framework and rendering engine           |
+| Rich              | ≥ 14.0            | Terminal rendering (Textual dependency)      |
+| Biopython         | ≥ 1.87            | GenBank parsing and NCBI Entrez fetch        |
+| primer3-py        | ≥ 2.3.0           | Primer design (Tm, thermodynamic screening)  |
+| pytest            | ≥ 9.0             | Test suite (dev only)                        |
+| pytest-asyncio    | ≥ 1.3             | Async test support (dev only)                |
+| **pLannotate**    | optional, conda   | Automatic plasmid annotation (`Shift+A`)     |
+| **BLAST+**        | optional, conda   | Required by pLannotate                       |
+| **Primer3 CLI**   | optional, `apt`   | Not used directly — primer3-py bundles it    |
+
+---
+
+## Data files
+
+All user data persists as human-readable JSON in the repo directory:
+
+| File                  | Purpose                                     |
+|-----------------------|---------------------------------------------|
+| `plasmid_library.json`| Saved plasmid collection (GenBank + metadata) |
+| `parts_bin.json`      | User-domesticated Golden Braid parts        |
+| `primers.json`        | Designed primer library                     |
+| `*.json.bak`          | Automatic backup — written before each save |
+
+These files are in `.gitignore` — they're user-local data, not repo content.
+A manual backup rotation happens on every save so accidental data loss is
+always recoverable via the `.bak` file.
+
+---
+
+## Tests
+
+```bash
+python3 -m pytest -q          # full suite (246 tests, ~45 s)
+python3 -m pytest tests/test_dna_sanity.py    # biology correctness only (< 1s)
+```
+
+---
+
+## License
+
+MIT

splicecraft-0.2.0.dist-info/RECORD

@@ -0,0 +1,6 @@
+splicecraft.py,sha256=xZDyMqXTXzRRKtW9FcC3bQF5QTjs_ykagGwuObRZ6Vc,306228
+splicecraft-0.2.0.dist-info/METADATA,sha256=aDAuu85OyzeWFbWXm_8KmI0zfxhN7TaIrItDUwlQ9PE,14497
+splicecraft-0.2.0.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
+splicecraft-0.2.0.dist-info/entry_points.txt,sha256=hlsNo4zfMMOW7R83IMp41R-kgkbcVETuA70ZKqowevA,49
+splicecraft-0.2.0.dist-info/licenses/LICENSE,sha256=9CoLZDw87mJTrQ3lcL5WW4nWc6iEyPHtY6TneCzVCTA,1070
+splicecraft-0.2.0.dist-info/RECORD,,

splicecraft-0.2.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.29.0
+Root-Is-Purelib: true
+Tag: py3-none-any

splicecraft-0.2.0.dist-info/entry_points.txt

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+[console_scripts]
+splicecraft = splicecraft:main

splicecraft-0.2.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Binomica Labs
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.