From 434b9b63eec1d9a321c1b5050f56fb2a32564034 Mon Sep 17 00:00:00 2001 From: turtlebasket Date: Sun, 29 Jan 2023 13:45:24 -0800 Subject: [PATCH] gff test --- gff-test/.gitignore | 136 ++++++++++++++++++++++++++++++++++++++++++ gff-test/README.md | 1 + gff-test/get-data.sh | 4 ++ gff-test/index.js | 14 +++++ gff-test/package.json | 12 ++++ gff-test/yarn.lock | 49 +++++++++++++++ 6 files changed, 216 insertions(+) create mode 100644 gff-test/.gitignore create mode 100644 gff-test/README.md create mode 100755 gff-test/get-data.sh create mode 100644 gff-test/index.js create mode 100644 gff-test/package.json create mode 100644 gff-test/yarn.lock diff --git a/gff-test/.gitignore b/gff-test/.gitignore new file mode 100644 index 0000000..6e857f0 --- /dev/null +++ b/gff-test/.gitignore @@ -0,0 +1,136 @@ +*.zip +ncbi_dataset/ + + + + +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +lerna-debug.log* +.pnpm-debug.log* + +# Diagnostic reports (https://nodejs.org/api/report.html) +report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json + +# Runtime data +pids +*.pid +*.seed +*.pid.lock + +# Directory for instrumented libs generated by jscoverage/JSCover +lib-cov + +# Coverage directory used by tools like istanbul +coverage +*.lcov + +# nyc test coverage +.nyc_output + +# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files) +.grunt + +# Bower dependency directory (https://bower.io/) +bower_components + +# node-waf configuration +.lock-wscript + +# Compiled binary addons (https://nodejs.org/api/addons.html) +build/Release + +# Dependency directories +node_modules/ +jspm_packages/ + +# Snowpack dependency directory (https://snowpack.dev/) +web_modules/ + +# TypeScript cache +*.tsbuildinfo + +# Optional npm cache directory +.npm + +# Optional eslint cache +.eslintcache + +# Optional stylelint cache +.stylelintcache + +# Microbundle cache +.rpt2_cache/ +.rts2_cache_cjs/ +.rts2_cache_es/ +.rts2_cache_umd/ + +# Optional REPL history +.node_repl_history + +# Output of 'npm pack' +*.tgz + +# Yarn Integrity file +.yarn-integrity + +# dotenv environment variable files +.env +.env.development.local +.env.test.local +.env.production.local +.env.local + +# parcel-bundler cache (https://parceljs.org/) +.cache +.parcel-cache + +# Next.js build output +.next +out + +# Nuxt.js build / generate output +.nuxt +dist + +# Gatsby files +.cache/ +# Comment in the public line in if your project uses Gatsby and not Next.js +# https://nextjs.org/blog/next-9-1#public-directory-support +# public + +# vuepress build output +.vuepress/dist + +# vuepress v2.x temp and cache directory +.temp +.cache + +# Docusaurus cache and generated files +.docusaurus + +# Serverless directories +.serverless/ + +# FuseBox cache +.fusebox/ + +# DynamoDB Local files +.dynamodb/ + +# TernJS port file +.tern-port + +# Stores VSCode versions used for testing VSCode extensions +.vscode-test + +# yarn v2 +.yarn/cache +.yarn/unplugged +.yarn/build-state.yml +.yarn/install-state.gz +.pnp.* diff --git a/gff-test/README.md b/gff-test/README.md new file mode 100644 index 0000000..1160276 --- /dev/null +++ b/gff-test/README.md @@ -0,0 +1 @@ +# GFF3 Format Support diff --git a/gff-test/get-data.sh b/gff-test/get-data.sh new file mode 100755 index 0000000..4d6cb20 --- /dev/null +++ b/gff-test/get-data.sh @@ -0,0 +1,4 @@ +mkdir -p data && \ + curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_000157115.2/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCF_000157115.2.zip" -H "Accept: application/zip" && \ + unzip -j GCF_000157115.2.zip ncbi_dataset/ ./ncbi_dataset/ && \ + rm GCF_000157115.2.zip diff --git a/gff-test/index.js b/gff-test/index.js new file mode 100644 index 0000000..6a7cc3c --- /dev/null +++ b/gff-test/index.js @@ -0,0 +1,14 @@ +const gff = require("@gmod/gff").default; +const fs = require('fs'); + +let items = 20; + +fs.createReadStream("./ncbi_dataset/data/GCF_000157115.2/genomic.gff") + .pipe(gff.parseStream({parseAll: true})) + .on('data', data => { + if (items > 0) { + console.log(data); + items -= 1; + } + else process.exit(0); + }) diff --git a/gff-test/package.json b/gff-test/package.json new file mode 100644 index 0000000..f9c99a2 --- /dev/null +++ b/gff-test/package.json @@ -0,0 +1,12 @@ +{ + "name": "gff-test", + "version": "0.1.0", + "main": "index.js", + "license": "MIT", + "scripts": { + "start": "node index.js" + }, + "dependencies": { + "@gmod/gff": "^1.3.0" + } +} diff --git a/gff-test/yarn.lock b/gff-test/yarn.lock new file mode 100644 index 0000000..d0a0310 --- /dev/null +++ b/gff-test/yarn.lock @@ -0,0 +1,49 @@ +# THIS IS AN AUTOGENERATED FILE. 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