{ "name": "aminosee", "version": "1.28.5", "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": "Allows genomics researchers to convert any file containing ASCII blocks of DNA (Fasta, GBK, .txt) into an image. A unique visualisation of DNA / RNA residing in text files, AminoSee is a way to render arbitrarily large files - due to support for streamed processing - into a static size PNG image using a pseudo-Hilbert infinite space filling curve written in the 18th century! Computation is done locally, and the files do not leave your machine. A back-end terminal daemon cli command that can be scripted is combined with a front-end GUI with 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. In a diectory with DNA files try running aminosee *. Alternatively use the GUI to Drag and drop files to render a unique colour view of RNA or DNA stored in text files, output to PNG graphics file, then launches an WebGL browser that projects the image onto a 3D Hilbert curve for immersive viewing, using THREEjs. Command line options alow one to filter by peptide.", "main": "./bin/aminosee.js", "bin": { "aminosee": "./bin/aminosee" }, "build": { "productName": "aminosee", "appId": "nz.funk.aminosee", "copyright": "Copyright © 2018-2019 Tom Atkinson", "icon": "src/public/favicon.png", "directories": [ "src/public/*", "src/public/fonts/*", "src/*" ], "mac": { "category": [ "public.app-category.education", "public.app-category.medical" ] } }, "scripts": { "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-old": "./build-lib.sh ; ./build-gui.sh ; nice time npm run build-web ; nice time npm run pkg", "build-all": "./run-test.sh --quiet ; ./build-lib.sh ; npm run pkg; ", "build-web": "npm run genversion ; npm run browserify ; npm run minify ; npm run credits", "genversion": "genversion src/aminosee-version.js", "browserify": "echo DISABLED browserify bin/aminosee.js -o bin/bundle.js", "minify": "uglify bin/bundle.js -o bin/bundle.min.js", "update": "./update.sh", "pkg": "nice npm run win32 ; nice npm run _macos ; nice npm run _linux ; nice npm run _win64", "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 . --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": { "autocannon": "^4.6.0", "chalk": "^2.4.2", "fs-extra": "^8.1.0", "genversion": "^2.2.0", "hammerjs": "^2.0.8", "http-server": "^0.12.1", "node-fetch": "^2.6.0", "open": "^6.4.0", "phoenix": "^1.4.16", "preferences": "^1.0.2", "terminal-kit": "^1.35.2", "three": "^0.106.2", "vows": "^0.8.3", "xterm": "^3.14.5" }, "devDependencies": { "@gmod/indexedfasta": "^1.0.13", "ascii-histogram": "^1.2.1", "async": "^3.2.0", "async-kit": "^2.2.4", "body-parser": "^1.19.0", "browser-resolve": "^1.11.3", "browserify": "^16.5.1", "bytes": "^3.1.0", "carlo": "^0.9.46", "cross-spawn": "^6.0.5", "cucumber": "^5.1.0", "cypress": "^3.8.3", "dat.gui": "^0.7.7", "ecstatic": "^4.1.4", "eslint": "^6.8.0", "eslint-config-rallycoding": "^3.2.0", "event-stream": "^4.0.1", "get-cursor-position": "^1.0.5", "hilbert-2d": "0.0.1", "humanize-duration": "^3.22.0", "husky": "^3.1.0", "internal-ip": "^4.3.0", "json-beautify": "^1.1.1", "keypress": "^0.2.1", "lazyness": "^1.1.1", "local-web-server": "^3.0.7", "minimist": "^1.2.5", "node-gyp": "^5.1.0", "node-pty": "^0.8.1", "npm-merge-driver": "^2.3.6", "parse-apache-directory-index": "^1.2.1", "pkg": "^4.4.5", "png.js": "^0.2.1", "pngjs": "^3.4.0", "remove": "^0.1.5", "request": "^2.88.2", "save": "^2.4.0", "serve": "^11.3.0", "serve-handler": "^6.1.2", "sliced": "^1.0.1", "spdy": "^4.0.2", "stream-file": "^0.2.4", "systeminformation": "^4.23.1", "tcp-port-used": "^1.0.1", "through": "^2.3.8", "uniq": "^1.0.1", "webpack-node-externals": "^1.7.2", "xmlhttprequest": "^1.8.0" }, "keywords": [ "dna", "genomics", "visualisation", "renderer", "genetics", "bioinformatics", "bionode", "amino acids", "peptides", "codons" ], "pkg": { "targets": [ "node10", "linux", "macos", "win" ], "scripts": [ "dist/root/pos.node", "src/*.js" ], "assets": [ "bin/*/**", "bin/pos.node", "node_modules/opn/**", "node_modules/terminal-kit/**", "node_modules/get-cursor-position/**", "node_modules/opn/xdg-open", "src/public/*", "src/public/fonts/*", "src/*", "package.json" ] } }