{ "name": "aminosee", "version": "1.32.8", "owner": "Thomas Bieder Atkinson", "author": "Tom Atkinson ", "website": "http://aminosee.funk.nz", "license": "GPL-3.0-only", "repository": { "type": "git", "url": "git://github.com/tomachinz/AminoSee.git" }, "description": "A unique visualisation of any large chunk of DNA or RNA residing in ASCII text files (such as FASTA, GBK etc and also just .txt like my hand-made test files), AminoSee is a way to render huge genomics files into a left-to-right top-bottom PNG linear image, a 2D infinite space filling square curve from 18th century, and a 3D hilbert curve from this century! Computation is done locally, without the files leaving your machine. A back-end terminal daemon cli command that can be scripted is combined with a front-end GUI using the Carlo, AminoSee features asynchronous streaming processing enabling arbitrary size files to be processed. It has been tested with files in excess of 4 GB and does not need the whole file in memory at any time. Try running 'aminosee *' in a directory with DNA files, or better run the batch script 'batch-peptides.sh'. The folder 'dna' is provided for bulk rendering it already has those scripts present. The GUI is not finished at this time. it is using THREEjs and a 3D Hilbert Curve, Carlo. Command line options allow one to filter by peptide, for example 'aminosee * --peptide=Ochre'. Allows genomics researchers to convert any file containing blocks of text format DNA (Fasta, GBK, .txt) into an interactive experience.", "main": "./bin/aminosee", "bin": { "aminosee": "./bin/aminosee" }, "build": { "productName": "aminosee", "appId": "nz.funk.aminosee", "copyright": "Copyright © 2018-2020 Tom Atkinson", "icon": "src/public/favicon.png", "directories": [ "src/public/*", "src/*" ], "mac": { "category": [ "public.app-category.education", "public.app-category.medical" ] } }, "scripts": { "postpublish": "PACKAGE_VERSION=$(cat package.json | grep \\\"version\\\" | head -1 | awk -F: '{ print $2 }' | sed 's/[\",]//g' | tr -d '[[:space:]]') && git tag v$PACKAGE_VERSION && git push --tags", "cypress": "node_modules/.bin/cypress open", "demo": "node bin/aminosee demo", "credits": "./build-credits.sh", "clean": "rimraf ./dist ./build", "crash": "node --inspect 27MB_TestPattern.txt --peptide=Ochre 3MB_TestPattern.txt 50KB_TestPattern.txt batch-peptides.sh batch-process.sh Gorilla_gorGor4_chr2B.fa", "eslint": "eslint src/aminosee-cli.js > test/eslint-errors.txt ; tail -n 64 test/eslint-errors.txt", "gource": "./gource.sh", "test": "echo 'requires cli programs: time, lighthouse, vows etc' ; time ./run-test.sh --quiet ;", "start": "node bin/aminosee", "serve": "node ./bin/aminosee", "inspect": "node --inspect bin/aminosee.js dna/27MB_TestPattern.txt /Volumes/aminosee/dna/Brown_Kiwi_NW_013982187v1.fa /Volumes/aminosee/dna/Brown_Kiwi_NW_013982187v1.fa -f -c1000 -vd --debug", "inspect2": "node --inspect bin/aminosee.js dna/50KB_TestPattern.txt -f -vd --debug", "build": "nice npm run build-web ; nice time npm run macos", "build-all": "./run-test.sh --quiet ; ./build-web.sh ; npm run pkg; ", "build-web": "npm run credits; npm run genversion ; npm run browserify ; npm run minify ;", "genversion": "genversion src/aminosee-version.js", "browserify": "echo DISABLED browserify bin/aminosee.js -o bin/aminosee.bundle.js", "minify": "echo DISABLED uglify bin/aminosee.bundle.js -o bin/aminosee.min.js", "update": "./update.sh", "pkg": "nice npm run win32 ; nice npm run _macos ; nice npm run _linux ; nice npm run _win64; nice npm run zip", "zip": "zip -8 -r ./dist/AminoSee_macos.zip ./dist/AminoSee_macos ; nice zip -8 -r ./dist/AminoSee_win.zip ./dist/AminoSee_win ; nice zip -8 -r ./dist/AminoSee_linux.zip ./dist/AminoSee_linux", "runmac": "time ./dist/AminoSee_macos/aminosee --demo -m9", "runlinux": "open ./dist/AminoSee_linux/aminosee --test -m9", "macos": "echo MACOS ; pkg . --build --targets macos --output ./dist/AminoSee_macos/aminosee ; ./dist/AminoSee_macos/aminosee", "win32": "echo WIN32 ; pkg . --targets win-x86 --output ./dist/AminoSee_win/aminosee-win32.exe", "win64": "echo WIN64 ; pkg . --targets win-x64 --output ./dist/AminoSee_win/aminosee.exe", "linux": "echo LINUX ; pkg . --targets linux --output ./dist/AminoSee_linux/aminosee ; ./dist/AminoSee_linux/aminosee", "_macos": "echo MACOS ; pkg . --targets macos --output ./dist/AminoSee_macos/aminosee ; zip -8 -r ./dist/AminoSee_macos.zip ./dist/AminoSee_macos", "_win32": "echo WIN32 ; pkg . --targets win-x86 --output ./dist/AminoSee_win/aminosee-win32.exe ;", "_win64": "echo WIN64 ; pkg . --targets win-x64 --output ./dist/AminoSee_win/aminosee.exe ; zip -8 -r ./dist/AminoSee_win.zip ./dist/AminoSee_win", "_linux": "echo LINUX ; pkg . --targets linux --output ./dist/AminoSee_linux/aminosee ; zip -8 -r ./dist/AminoSee_linux.zip ./dist/AminoSee_linux" }, "dependencies": { "@neutralinojs/neu": "^1.7.0", "async-kit": "^2.2.4", "autocannon": "^4.6.0", "bcrypt": "^5.0.0", "chalk": "^2.4.2", "describe": "^1.2.0", "fs-extra": "^8.1.0", "genversion": "^2.2.1", "hammerjs": "^2.0.8", "hilbert-2d": "0.0.1", "http-server": "^0.12.3", "internal-ip": "^4.3.0", "json-beautify": "^1.1.1", "node-fetch": "^2.6.1", "open": "^6.4.0", "parallax-js": "^3.1.0", "phoenix": "^1.5.6", "preferences": "^1.0.2", "terminal-kit": "^1.43.0", "three": "^0.118.3", "vows": "^0.8.3", "xmlhttprequest": "^1.8.0", "xterm": "^4.9.0" }, "devDependencies": { "@gmod/indexedfasta": "^1.0.13", "ascii-histogram": "^1.2.1", "async": "^3.2.0", "body-parser": "^1.19.0", "browser-resolve": "^1.11.3", "browserify": "^16.5.2", "bytes": "^3.1.0", "carlo": "^0.9.46", "cross-spawn": "^6.0.5", "cucumber": "^5.1.0", "cypress": "^5.4.0", "dat.gui": "^0.7.7", "ecstatic": "^4.1.4", "eslint": "^7.11.0", "eslint-config-rallycoding": "^3.2.0", "event-stream": "^4.0.1", "get-cursor-position": "^1.0.5", "humanize-duration": "^3.24.0", "husky": "^3.1.0", "keypress": "^0.2.1", "lazyness": "^1.2.0", "local-web-server": "^4.2.1", "minimist": "^1.2.5", "node-gyp": "^5.1.1", "node-pty": "^0.8.1", "npm-merge-driver": "^2.3.6", "parse-apache-directory-index": "^1.2.1", "pkg": "^4.4.9", "png.js": "^0.2.1", "pngjs": "^3.4.0", "remove": "^0.1.5", "request": "^2.88.2", "save": "^2.4.0", "serve": "^11.3.2", "serve-handler": "^6.1.3", "sliced": "^1.0.1", "spdy": "^4.0.2", "stream-file": "^0.2.4", "systeminformation": "^4.27.9", "tcp-port-used": "^1.0.1", "through": "^2.3.8", "uniq": "^1.0.1", "webpack-node-externals": "^1.7.2" }, "keywords": [ "dna", "genomics", "visualisation", "renderer", "genetics", "bioinformatics", "bionode", "amino acids", "peptides", "codons" ], "pkg": { "targets": [ "node10", "linux", "macos", "win" ], "scripts": [], "assets": [ "node_modules/terminal-kit/lib/Palette.js", "node_modules/terminal-kit/lib/image.js", "node_modules/hilbert-2d/hilbert.js", "node_modules/terminal-kit/lib/termconfig", "node_modules/terminal-kit/lib/colorScheme", "node_modules/open/xdg-open", "src/*", "src/public/*", "package.json" ] } }