gff test
commit
434b9b63ee
|
|
@ -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.*
|
||||
|
|
@ -0,0 +1 @@
|
|||
# GFF3 Format Support
|
||||
|
|
@ -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
|
||||
|
|
@ -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);
|
||||
})
|
||||
|
|
@ -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"
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
|
||||
# yarn lockfile v1
|
||||
|
||||
|
||||
"@gmod/gff@^1.3.0":
|
||||
version "1.3.0"
|
||||
resolved "https://registry.yarnpkg.com/@gmod/gff/-/gff-1.3.0.tgz#d231a6f807cfb8f191c26c6410021c17155e4093"
|
||||
integrity sha512-OjEnQLR6iIcrau603blFfUkmnWGDVfOu/LQoJNa7TsvKnjWlHYPlvqb5h2IV7wI+zElDY648mQ9zrElt2uR80A==
|
||||
dependencies:
|
||||
stream-browserify "^3.0.0"
|
||||
|
||||
inherits@^2.0.3, inherits@~2.0.4:
|
||||
version "2.0.4"
|
||||
resolved "https://registry.yarnpkg.com/inherits/-/inherits-2.0.4.tgz#0fa2c64f932917c3433a0ded55363aae37416b7c"
|
||||
integrity sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ==
|
||||
|
||||
readable-stream@^3.5.0:
|
||||
version "3.6.0"
|
||||
resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-3.6.0.tgz#337bbda3adc0706bd3e024426a286d4b4b2c9198"
|
||||
integrity sha512-BViHy7LKeTz4oNnkcLJ+lVSL6vpiFeX6/d3oSH8zCW7UxP2onchk+vTGB143xuFjHS3deTgkKoXXymXqymiIdA==
|
||||
dependencies:
|
||||
inherits "^2.0.3"
|
||||
string_decoder "^1.1.1"
|
||||
util-deprecate "^1.0.1"
|
||||
|
||||
safe-buffer@~5.2.0:
|
||||
version "5.2.1"
|
||||
resolved "https://registry.yarnpkg.com/safe-buffer/-/safe-buffer-5.2.1.tgz#1eaf9fa9bdb1fdd4ec75f58f9cdb4e6b7827eec6"
|
||||
integrity sha512-rp3So07KcdmmKbGvgaNxQSJr7bGVSVk5S9Eq1F+ppbRo70+YeaDxkw5Dd8NPN+GD6bjnYm2VuPuCXmpuYvmCXQ==
|
||||
|
||||
stream-browserify@^3.0.0:
|
||||
version "3.0.0"
|
||||
resolved "https://registry.yarnpkg.com/stream-browserify/-/stream-browserify-3.0.0.tgz#22b0a2850cdf6503e73085da1fc7b7d0c2122f2f"
|
||||
integrity sha512-H73RAHsVBapbim0tU2JwwOiXUj+fikfiaoYAKHF3VJfA0pe2BCzkhAHBlLG6REzE+2WNZcxOXjK7lkso+9euLA==
|
||||
dependencies:
|
||||
inherits "~2.0.4"
|
||||
readable-stream "^3.5.0"
|
||||
|
||||
string_decoder@^1.1.1:
|
||||
version "1.3.0"
|
||||
resolved "https://registry.yarnpkg.com/string_decoder/-/string_decoder-1.3.0.tgz#42f114594a46cf1a8e30b0a84f56c78c3edac21e"
|
||||
integrity sha512-hkRX8U1WjJFd8LsDJ2yQ/wWWxaopEsABU1XfkM8A+j0+85JAGppt16cr1Whg6KIbb4okU6Mql6BOj+uup/wKeA==
|
||||
dependencies:
|
||||
safe-buffer "~5.2.0"
|
||||
|
||||
util-deprecate@^1.0.1:
|
||||
version "1.0.2"
|
||||
resolved "https://registry.yarnpkg.com/util-deprecate/-/util-deprecate-1.0.2.tgz#450d4dc9fa70de732762fbd2d4a28981419a0ccf"
|
||||
integrity sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==
|
||||
Loading…
Reference in New Issue