diff --git a/.gitignore b/.gitignore index bd5f33a8..bc79950e 100644 --- a/.gitignore +++ b/.gitignore @@ -47,3 +47,6 @@ pkg # For rubinius: #*.rbc + +node_modules/** +dist/** diff --git a/.nvmrc b/.nvmrc new file mode 100644 index 00000000..2bd5a0a9 --- /dev/null +++ b/.nvmrc @@ -0,0 +1 @@ +22 diff --git a/VERSION b/VERSION deleted file mode 100644 index fd2a0186..00000000 --- a/VERSION +++ /dev/null @@ -1 +0,0 @@ -3.1.0 diff --git a/bin/uniprot.ts b/bin/uniprot.ts new file mode 100755 index 00000000..bbe9aab0 --- /dev/null +++ b/bin/uniprot.ts @@ -0,0 +1,71 @@ +#!/usr/bin/env node + +import { Option, program } from 'commander'; +import { createInterface } from 'node:readline'; +import { version } from '../package.json'; + +const VALID_FORMATS = ["fasta", "gff", "json", "rdf", "sequence", "xml"]; + +const description = `Command line interface to UniProt web services. + +The uniprot command fetches UniProt entries from the UniProt web services. The command expects a list of UniProt Accession Numbers that are passed + +- as separate command line arguments +- to standard input + +The command will give priority to the first way UniProt Accession Numbers are passed, in the order as listed above. The standard input should have one UniProt Accession Number per line. + +The uniprot command yields just the protein sequences as a default, but can return several formats.`; + +program + .version(version) + .summary("Command line interface to UniProt web services.") + .description(description) + .argument("[accessions...]", "UniProt Accession Numbers") + .addOption(new Option("-f, --format ", `output format`).choices(VALID_FORMATS).default("sequence")); + +program.parse(process.argv); +const format = program.opts().format; +const accessions = program.args; + +if (accessions.length !== 0) { // input from command line arguments + accessions.forEach(processUniprotEntry); +} else { // input from standard input + for await (const line of createInterface({ input: process.stdin })) { + processUniprotEntry(line.trim()); + }; +} + +/** + * Fetches a UniProt entry and writes it to standard output. + * + * @param accession UniProt Accession Number + */ +async function processUniprotEntry(accession: string) { + process.stdout.write(await getUniprotEntry(accession, format) + "\n"); +} + +/** + * Fetches a UniProt entry in the requested format. + * + * @param accession UniProt Accession Number + * @param format output format + * @returns UniProt entry in the requested format + */ +async function getUniprotEntry(accession: string, format: string): Promise { + // The UniProt REST API does not support the "sequence" format, so fetch fasta and remove the header + if (format === "sequence") { + return (await getUniprotEntry(accession, "fasta")) + .split("\n") + .slice(1) + .join(""); + } else { + const r = await fetch(`https://rest.uniprot.org/uniprotkb/${accession}.${format}`); + if (r.ok) { + return r.text(); + } else { + process.stderr.write(`Error fetching ${accession}: ${r.status} ${r.statusText}\n`); + return ""; + } + } +} diff --git a/package.json b/package.json new file mode 100644 index 00000000..74077291 --- /dev/null +++ b/package.json @@ -0,0 +1,25 @@ +{ + "name": "unipept-cli", + "version": "4.0.0", + "description": "Command line interface to the Unipept web services", + "repository": "git@github.com:unipept/unipept-cli.git", + "author": "Bart Mesuere ", + "license": "MIT", + "private": false, + "type": "module", + "bin": { + "uniprot": "./bin/uniprot.js" + }, + "scripts": { + "build": "yarn run tsc", + "uniprot": "yarn run tsx bin/uniprot.ts" + }, + "dependencies": { + "commander": "^12.1.0" + }, + "devDependencies": { + "@types/node": "^20.14.2", + "tsx": "^4.15.6", + "typescript": "^5.4.5" + } +} diff --git a/tsconfig.json b/tsconfig.json new file mode 100644 index 00000000..e101d71c --- /dev/null +++ b/tsconfig.json @@ -0,0 +1,11 @@ +{ + "include": [ + "bin/**/*" + ], + "compilerOptions": { + "outDir": "./dist", + "module": "NodeNext", + "strict": true, + "resolveJsonModule": true + } +} diff --git a/yarn.lock b/yarn.lock new file mode 100644 index 00000000..f6423ed5 --- /dev/null +++ b/yarn.lock @@ -0,0 +1,196 @@ +# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY. +# yarn lockfile v1 + + +"@esbuild/aix-ppc64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/aix-ppc64/-/aix-ppc64-0.21.5.tgz#c7184a326533fcdf1b8ee0733e21c713b975575f" + integrity sha512-1SDgH6ZSPTlggy1yI6+Dbkiz8xzpHJEVAlF/AM1tHPLsf5STom9rwtjE4hKAF20FfXXNTFqEYXyJNWh1GiZedQ== + +"@esbuild/android-arm64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/android-arm64/-/android-arm64-0.21.5.tgz#09d9b4357780da9ea3a7dfb833a1f1ff439b4052" + integrity sha512-c0uX9VAUBQ7dTDCjq+wdyGLowMdtR/GoC2U5IYk/7D1H1JYC0qseD7+11iMP2mRLN9RcCMRcjC4YMclCzGwS/A== + +"@esbuild/android-arm@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/android-arm/-/android-arm-0.21.5.tgz#9b04384fb771926dfa6d7ad04324ecb2ab9b2e28" + integrity sha512-vCPvzSjpPHEi1siZdlvAlsPxXl7WbOVUBBAowWug4rJHb68Ox8KualB+1ocNvT5fjv6wpkX6o/iEpbDrf68zcg== + +"@esbuild/android-x64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/android-x64/-/android-x64-0.21.5.tgz#29918ec2db754cedcb6c1b04de8cd6547af6461e" + integrity sha512-D7aPRUUNHRBwHxzxRvp856rjUHRFW1SdQATKXH2hqA0kAZb1hKmi02OpYRacl0TxIGz/ZmXWlbZgjwWYaCakTA== + +"@esbuild/darwin-arm64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/darwin-arm64/-/darwin-arm64-0.21.5.tgz#e495b539660e51690f3928af50a76fb0a6ccff2a" + integrity sha512-DwqXqZyuk5AiWWf3UfLiRDJ5EDd49zg6O9wclZ7kUMv2WRFr4HKjXp/5t8JZ11QbQfUS6/cRCKGwYhtNAY88kQ== + +"@esbuild/darwin-x64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/darwin-x64/-/darwin-x64-0.21.5.tgz#c13838fa57372839abdddc91d71542ceea2e1e22" + integrity sha512-se/JjF8NlmKVG4kNIuyWMV/22ZaerB+qaSi5MdrXtd6R08kvs2qCN4C09miupktDitvh8jRFflwGFBQcxZRjbw== + +"@esbuild/freebsd-arm64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/freebsd-arm64/-/freebsd-arm64-0.21.5.tgz#646b989aa20bf89fd071dd5dbfad69a3542e550e" + integrity sha512-5JcRxxRDUJLX8JXp/wcBCy3pENnCgBR9bN6JsY4OmhfUtIHe3ZW0mawA7+RDAcMLrMIZaf03NlQiX9DGyB8h4g== + +"@esbuild/freebsd-x64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/freebsd-x64/-/freebsd-x64-0.21.5.tgz#aa615cfc80af954d3458906e38ca22c18cf5c261" + integrity sha512-J95kNBj1zkbMXtHVH29bBriQygMXqoVQOQYA+ISs0/2l3T9/kj42ow2mpqerRBxDJnmkUDCaQT/dfNXWX/ZZCQ== + +"@esbuild/linux-arm64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-arm64/-/linux-arm64-0.21.5.tgz#70ac6fa14f5cb7e1f7f887bcffb680ad09922b5b" + integrity sha512-ibKvmyYzKsBeX8d8I7MH/TMfWDXBF3db4qM6sy+7re0YXya+K1cem3on9XgdT2EQGMu4hQyZhan7TeQ8XkGp4Q== + +"@esbuild/linux-arm@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-arm/-/linux-arm-0.21.5.tgz#fc6fd11a8aca56c1f6f3894f2bea0479f8f626b9" + integrity sha512-bPb5AHZtbeNGjCKVZ9UGqGwo8EUu4cLq68E95A53KlxAPRmUyYv2D6F0uUI65XisGOL1hBP5mTronbgo+0bFcA== + +"@esbuild/linux-ia32@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-ia32/-/linux-ia32-0.21.5.tgz#3271f53b3f93e3d093d518d1649d6d68d346ede2" + integrity sha512-YvjXDqLRqPDl2dvRODYmmhz4rPeVKYvppfGYKSNGdyZkA01046pLWyRKKI3ax8fbJoK5QbxblURkwK/MWY18Tg== + +"@esbuild/linux-loong64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-loong64/-/linux-loong64-0.21.5.tgz#ed62e04238c57026aea831c5a130b73c0f9f26df" + integrity sha512-uHf1BmMG8qEvzdrzAqg2SIG/02+4/DHB6a9Kbya0XDvwDEKCoC8ZRWI5JJvNdUjtciBGFQ5PuBlpEOXQj+JQSg== + +"@esbuild/linux-mips64el@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-mips64el/-/linux-mips64el-0.21.5.tgz#e79b8eb48bf3b106fadec1ac8240fb97b4e64cbe" + integrity sha512-IajOmO+KJK23bj52dFSNCMsz1QP1DqM6cwLUv3W1QwyxkyIWecfafnI555fvSGqEKwjMXVLokcV5ygHW5b3Jbg== + +"@esbuild/linux-ppc64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-ppc64/-/linux-ppc64-0.21.5.tgz#5f2203860a143b9919d383ef7573521fb154c3e4" + integrity sha512-1hHV/Z4OEfMwpLO8rp7CvlhBDnjsC3CttJXIhBi+5Aj5r+MBvy4egg7wCbe//hSsT+RvDAG7s81tAvpL2XAE4w== + +"@esbuild/linux-riscv64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-riscv64/-/linux-riscv64-0.21.5.tgz#07bcafd99322d5af62f618cb9e6a9b7f4bb825dc" + integrity sha512-2HdXDMd9GMgTGrPWnJzP2ALSokE/0O5HhTUvWIbD3YdjME8JwvSCnNGBnTThKGEB91OZhzrJ4qIIxk/SBmyDDA== + +"@esbuild/linux-s390x@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-s390x/-/linux-s390x-0.21.5.tgz#b7ccf686751d6a3e44b8627ababc8be3ef62d8de" + integrity sha512-zus5sxzqBJD3eXxwvjN1yQkRepANgxE9lgOW2qLnmr8ikMTphkjgXu1HR01K4FJg8h1kEEDAqDcZQtbrRnB41A== + +"@esbuild/linux-x64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/linux-x64/-/linux-x64-0.21.5.tgz#6d8f0c768e070e64309af8004bb94e68ab2bb3b0" + integrity sha512-1rYdTpyv03iycF1+BhzrzQJCdOuAOtaqHTWJZCWvijKD2N5Xu0TtVC8/+1faWqcP9iBCWOmjmhoH94dH82BxPQ== + +"@esbuild/netbsd-x64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/netbsd-x64/-/netbsd-x64-0.21.5.tgz#bbe430f60d378ecb88decb219c602667387a6047" + integrity sha512-Woi2MXzXjMULccIwMnLciyZH4nCIMpWQAs049KEeMvOcNADVxo0UBIQPfSmxB3CWKedngg7sWZdLvLczpe0tLg== + +"@esbuild/openbsd-x64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/openbsd-x64/-/openbsd-x64-0.21.5.tgz#99d1cf2937279560d2104821f5ccce220cb2af70" + integrity sha512-HLNNw99xsvx12lFBUwoT8EVCsSvRNDVxNpjZ7bPn947b8gJPzeHWyNVhFsaerc0n3TsbOINvRP2byTZ5LKezow== + +"@esbuild/sunos-x64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/sunos-x64/-/sunos-x64-0.21.5.tgz#08741512c10d529566baba837b4fe052c8f3487b" + integrity sha512-6+gjmFpfy0BHU5Tpptkuh8+uw3mnrvgs+dSPQXQOv3ekbordwnzTVEb4qnIvQcYXq6gzkyTnoZ9dZG+D4garKg== + +"@esbuild/win32-arm64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/win32-arm64/-/win32-arm64-0.21.5.tgz#675b7385398411240735016144ab2e99a60fc75d" + integrity sha512-Z0gOTd75VvXqyq7nsl93zwahcTROgqvuAcYDUr+vOv8uHhNSKROyU961kgtCD1e95IqPKSQKH7tBTslnS3tA8A== + +"@esbuild/win32-ia32@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/win32-ia32/-/win32-ia32-0.21.5.tgz#1bfc3ce98aa6ca9a0969e4d2af72144c59c1193b" + integrity sha512-SWXFF1CL2RVNMaVs+BBClwtfZSvDgtL//G/smwAc5oVK/UPu2Gu9tIaRgFmYFFKrmg3SyAjSrElf0TiJ1v8fYA== + +"@esbuild/win32-x64@0.21.5": + version "0.21.5" + resolved "https://registry.yarnpkg.com/@esbuild/win32-x64/-/win32-x64-0.21.5.tgz#acad351d582d157bb145535db2a6ff53dd514b5c" + integrity sha512-tQd/1efJuzPC6rCFwEvLtci/xNFcTZknmXs98FYDfGE4wP9ClFV98nyKrzJKVPMhdDnjzLhdUyMX4PsQAPjwIw== + +"@types/node@^20.14.2": + version "20.14.2" + resolved "https://registry.yarnpkg.com/@types/node/-/node-20.14.2.tgz#a5f4d2bcb4b6a87bffcaa717718c5a0f208f4a18" + integrity sha512-xyu6WAMVwv6AKFLB+e/7ySZVr/0zLCzOa7rSpq6jNwpqOrUbcACDWC+53d4n2QHOnDou0fbIsg8wZu/sxrnI4Q== + dependencies: + undici-types "~5.26.4" + +commander@^12.1.0: + version "12.1.0" + resolved "https://registry.yarnpkg.com/commander/-/commander-12.1.0.tgz#01423b36f501259fdaac4d0e4d60c96c991585d3" + integrity sha512-Vw8qHK3bZM9y/P10u3Vib8o/DdkvA2OtPtZvD871QKjy74Wj1WSKFILMPRPSdUSx5RFK1arlJzEtA4PkFgnbuA== + +esbuild@~0.21.4: + version "0.21.5" + resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.21.5.tgz#9ca301b120922959b766360d8ac830da0d02997d" + integrity sha512-mg3OPMV4hXywwpoDxu3Qda5xCKQi+vCTZq8S9J/EpkhB2HzKXq4SNFZE3+NK93JYxc8VMSep+lOUSC/RVKaBqw== + optionalDependencies: + "@esbuild/aix-ppc64" "0.21.5" + "@esbuild/android-arm" "0.21.5" + "@esbuild/android-arm64" "0.21.5" + "@esbuild/android-x64" "0.21.5" + "@esbuild/darwin-arm64" "0.21.5" + "@esbuild/darwin-x64" "0.21.5" + "@esbuild/freebsd-arm64" "0.21.5" + "@esbuild/freebsd-x64" "0.21.5" + "@esbuild/linux-arm" "0.21.5" + "@esbuild/linux-arm64" "0.21.5" + "@esbuild/linux-ia32" "0.21.5" + "@esbuild/linux-loong64" "0.21.5" + "@esbuild/linux-mips64el" "0.21.5" + "@esbuild/linux-ppc64" "0.21.5" + "@esbuild/linux-riscv64" "0.21.5" + "@esbuild/linux-s390x" "0.21.5" + "@esbuild/linux-x64" "0.21.5" + "@esbuild/netbsd-x64" "0.21.5" + "@esbuild/openbsd-x64" "0.21.5" + "@esbuild/sunos-x64" "0.21.5" + "@esbuild/win32-arm64" "0.21.5" + "@esbuild/win32-ia32" "0.21.5" + "@esbuild/win32-x64" "0.21.5" + +fsevents@~2.3.3: + version "2.3.3" + resolved "https://registry.yarnpkg.com/fsevents/-/fsevents-2.3.3.tgz#cac6407785d03675a2a5e1a5305c697b347d90d6" + integrity sha512-5xoDfX+fL7faATnagmWPpbFtwh/R77WmMMqqHGS65C3vvB0YHrgF+B1YmZ3441tMj5n63k0212XNoJwzlhffQw== + +get-tsconfig@^4.7.5: + version "4.7.5" + resolved "https://registry.yarnpkg.com/get-tsconfig/-/get-tsconfig-4.7.5.tgz#5e012498579e9a6947511ed0cd403272c7acbbaf" + integrity sha512-ZCuZCnlqNzjb4QprAzXKdpp/gh6KTxSJuw3IBsPnV/7fV4NxC9ckB+vPTt8w7fJA0TaSD7c55BR47JD6MEDyDw== + dependencies: + resolve-pkg-maps "^1.0.0" + +resolve-pkg-maps@^1.0.0: + version "1.0.0" + resolved "https://registry.yarnpkg.com/resolve-pkg-maps/-/resolve-pkg-maps-1.0.0.tgz#616b3dc2c57056b5588c31cdf4b3d64db133720f" + integrity sha512-seS2Tj26TBVOC2NIc2rOe2y2ZO7efxITtLZcGSOnHHNOQ7CkiUBfw0Iw2ck6xkIhPwLhKNLS8BO+hEpngQlqzw== + +tsx@^4.15.6: + version "4.15.6" + resolved "https://registry.yarnpkg.com/tsx/-/tsx-4.15.6.tgz#4522ed093f7fa54f031a7a999274e8b35dbf3165" + integrity sha512-is0VQQlfNZRHEuSSTKA6m4xw74IU4AizmuB6lAYLRt9XtuyeQnyJYexhNZOPCB59SqC4JzmSzPnHGBXxf3k0hA== + dependencies: + esbuild "~0.21.4" + get-tsconfig "^4.7.5" + optionalDependencies: + fsevents "~2.3.3" + +typescript@^5.4.5: + version "5.4.5" + resolved "https://registry.yarnpkg.com/typescript/-/typescript-5.4.5.tgz#42ccef2c571fdbd0f6718b1d1f5e6e5ef006f611" + integrity sha512-vcI4UpRgg81oIRUFwR0WSIHKt11nJ7SAVlYNIu+QpqeyXP+gpQJy/Z4+F0aGxSE4MqwjyXvW/TzgkLAx2AGHwQ== + +undici-types@~5.26.4: + version "5.26.5" + resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-5.26.5.tgz#bcd539893d00b56e964fd2657a4866b221a65617" + integrity sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==