Huge News!Announcing our $40M Series B led by Abstract Ventures.Learn More →
Socket
Sign inDemoInstall
Socket
Sign inDemoInstall

bionode-ncbi

Package Overview
Dependencies
Maintainers
3
Versions
49
Alerts
File Explorer

Advanced tools

License
Socket logo

Install Socket

Detect and block malicious and high-risk dependencies

Install

bionode-ncbi - npm Package Compare versions

Comparing version 1.7.0 to 2.0.0

31868/GCF_000010365.1_ASM1036v1_genomic.fna.gz
CONTRIBUTING.md

171

cli.js
#!/usr/bin/env node
var minimist = require('minimist')
var JSONStream = require('JSONStream')

@@ -7,70 +6,121 @@ var split = require('split2')

var insight = require('./lib/anonymous-tracking')
var argv = require('yargs')
.strict()
.demandCommand(1)
.version()
.help()
.alias('help', 'h')
.alias('verbose', 'v')
.epilogue('For more information, check our documentation at http://doc.bionode.io')
.usage('Usage: bionode-ncbi <command> [arguments] --limit [num] --pretty')
.command(
'search <db> [term]',
`Takes a database name and a query term. Returns the metadata.`
)
.example('search', `taxonomy 'solenopsis invicta'`)
.example('search', `sra human --limit 1 --pretty`)
.command(
'fetch <db> [term]',
`Takes a database name and a query term. Returns the data.`
)
.example('fetch', `nucest p53 -l 1 --pretty`)
.command(
'urls <dlsource> [term]',
`Takes either sra or assembly db name and query term. Returns URLs of datasets.`
)
.example('urls', `sra solenopsis invicta`)
.example('urls', `assembly solenopsis invicta | json genomic.fna`)
.command(
'download <dlsource> [term]',
`Takes either sra or assembly db name and query term. Downloads the corresponding \
SRA or assembly (genomic.fna) file into a folder named after the unique ID (UID).`
)
.example('download', `assembly solenopsis invicta --pretty`)
.command(
'link <srcDB> <destDB> [srcUID]',
`Returns a unique ID (UID) from a destination database linked to another UID \
from a source database.`
)
.example('link', `assembly bioproject 244018 --pretty`)
.command(
'expand <property> [destProperty]',
`Takes a property (e.g. biosample) and an optional destination property
(e.g. sample) and looks for a field named property+id (e.g. biosampleid)
in the Streamed object. Then it will do a ncbi.search for that id and save the
result under Streamed object.property.`
)
.example('expand',
`bionode-ncbi search genome 'solenopsis invicta' -l 1 | \\
bionode-ncbi expand tax -s --pretty`
)
.command(
'plink <property> <destDB>',
`Similar to Link but takes the srcUID from a property of the Streamed object
and attaches the result to a property with the name of the destination DB.`
)
.example('plink',
`bionode-ncbi search genome 'solenopsis invicta' -l 1 | \\
bionode-ncbi expand tax -s | \\
bionode-ncbi plink tax sra -s --pretty`
)
.alias('stdin', 's')
.boolean('stdin')
.describe('stdin', 'Read STDIN')
.alias('limit', 'l')
.number('limit')
.describe('limit', 'Limit number of results')
.alias('throughput', 't')
.number('throughput')
.describe('throughput', 'Number of items per API request')
.alias('pretty', 'p')
.boolean('pretty')
.describe('pretty', 'Print human readable output instead of NDJSON')
.choices('dlsource', ['assembly', 'sra'])
.choices('db', [
'gquery', 'assembly', 'bioproject', 'biosample', 'biosystems', 'books',
'clinvar', 'clone', 'cdd', 'gap', 'dbvar', 'nucest', 'gene', 'genome', 'gds',
'geoprofiles', 'nucgss', 'gtr', 'homologene', 'medgen', 'mesh', 'ncbisearch',
'nlmcatalog', 'nuccore', 'omim', 'pmc', 'popset', 'probe', 'protein',
'proteinclusters', 'pcassay', 'pccompound', 'pcsubstance', 'pubmed',
'pubmedhealth', 'snp', 'sparcle', 'sra', 'structure', 'taxonomy', 'toolkit',
'toolkitall', 'toolkitbook', 'toolkitbookgh', 'unigene'
])
.example('databases available',
`gquery (All Databases), assembly, bioproject, biosample, biosystems, \
books, clinvar, clone, cdd (Conserved Domains), gap (dbGaP), dbvar, \
nucest (EST), gene, genome, gds (GEO DataSets), geoprofiles (GEO Profiles), \
nucgss (GSS), gtr (GTR), homologene, medgen, mesh, \
ncbisearch (NCBI Web Site), nlmcatalog, nuccore (Nucleotide), omim, pmc, \
popset, probe, protein, proteinclusters, pcassay (PubChem BioAssay), \
pccompound (PubChem Compound), pcsubstance (PubChem Substance), \
pubmed, pubmedhealth, snp, sparcle, sra, structure, \
taxonomy, toolkit, toolkitall, toolkitbook, toolkitbookgh, unigene`
)
.example(`DEBUG mode: export DEBUG='*'`)
.argv
if (argv.dlsource) { argv.db = argv.dlsource }
insight.track('ncbi', 'cli')
var minimistOptions = {
alias: {
limit: 'l',
throughput: 't',
help: 'h'
}
}
var ncbiStream = ncbi[argv._[0]](argv)
var jsonPattern = /\{(.+?)\}/,
args = process.argv.slice(2).join(' '),
options = {},
match = args.match(jsonPattern)
if (match) {
var jsonLine = match[0].replace(/\'/g, '\"'),
options = JSON.parse(jsonLine),
args = args.replace(match[0], 'obj')
}
var argv = minimist(args.split(' '), minimistOptions)
if (argv.help || argv._.length === 0) {
console.log('Please check the documentation at http://doc.bionode.io')
process.exit()
}
var command = argv._[0]
var arg1 = argv._[1]
var lastArg = argv._[argv._.length - 1]
var wantsStdin = false
if (lastArg === '-') {
wantsStdin = true
argv._.pop()
}
if (command === 'link') {
var arg2 = argv._[2]
var arg3 = argv._[3]
var jsonStream
if (argv.pretty) {
jsonStream = JSONStream.stringify(false, null, null, 2)
} else {
var arg2 = argv._.slice(2).join(' ')
var arg3 = null
jsonStream = JSONStream.stringify(false)
}
if (Object.keys(argv).length > 1) {
options.limit = argv.limit
options.throughput = argv.throughput
ncbiStream.pipe(jsonStream).pipe(process.stdout)
if (arg1 !== 'obj') {
options.db = arg1
options.term = arg2
}
}
var ncbiStream = Object.keys(options).length ? ncbi[command](options) : ncbi[command](arg1, arg2, arg3)
ncbiStream.pipe(JSONStream.stringify(false)).pipe(process.stdout)
if (wantsStdin) {
if (argv.stdin) {
insight.track('ncbi', 'stdin')
process.stdin.setEncoding('utf8')
process.stdin.pipe(split()).on('data', function (data) {
if (data.trim() === '') { return }
ncbiStream.write(data.trim())
})
process.stdin
.pipe(split())
.pipe(JSONStream.parse())
.pipe(ncbiStream)
process.stdin.on('end', function () {

@@ -84,1 +134,6 @@ ncbiStream.end()

})
ncbiStream.on('error', function (error) {
console.error(error.message)
process.exit()
})

10

lib/anonymous-tracking.js
// Anonymous usage metrics for debug and funding, if user agrees
const Insight = require('insight');
const pkg = require('../package.json');
const Insight = require('insight')
const pkg = require('../package.json')

@@ -9,7 +9,7 @@ const insight = new Insight({

pkg
});
})
if (insight.optOut === undefined) {
insight.askPermission("Bionode is open and free. Can we anonymously report usage statistics for improvement and funding purposes?");
insight.askPermission('Bionode is open and free. Can we anonymously report usage statistics for improvement and funding purposes?')
}
module.exports = insight
module.exports = insight

106

lib/bionode-ncbi.js

@@ -17,7 +17,7 @@ // # bionode-ncbi

//
// # bionode-ncbi [command] [arguments] --limit (-l) --throughput (-t)
// # bionode-ncbi [command] [arguments] --limit (-l) --throughput (-t) --pretty (-p)
// $ bionode-ncbi search taxonomy solenopsis
// $ bionode-ncbi search sra human --limit 500 # only return 500 items
// $ bionode-ncbi search sra human --throughput 250 # fetch 250 items per API request
// $ bionode-ncbi download assembly solenopsis invicta
// $ bionode-ncbi download assembly solenopsis invicta --pretty # returns a simple progress bar to stdout
// $ bionode-ncbi urls sra solenopsis invicta

@@ -54,3 +54,3 @@ // $ bionode-ncbi link assembly bioproject 244018

'biosample': ['sampledata'],
'assembly': ['meta' ]
'assembly': ['meta']
}

@@ -113,3 +113,3 @@ var LASTSTREAM = {

insight.track('ncbi', 'search')
var opts = typeof db === 'string' ? { db: db, term: term } : db
var opts = typeof db === 'string' ? { db, term } : db
cb = typeof term === 'function' ? term : cb

@@ -156,5 +156,5 @@

var esearchRes = obj.body.esearchresult
if (esearchRes === undefined
|| esearchRes.webenv === undefined
|| esearchRes.count === undefined) {
if (esearchRes === undefined ||
esearchRes.webenv === undefined ||
esearchRes.count === undefined) {
var msg = 'NCBI returned invalid results, this could be a temporary' +

@@ -250,4 +250,5 @@ ' issue with NCBI servers.\nRequest URL: ' + obj.url

insight.track('ncbi', 'link')
var opts = typeof srcDB === 'string' ? { srcDB, destDB, srcUID } : srcDB
var stream = pumpify.obj(
createAPILinkURL(srcDB, destDB),
createAPILinkURL(opts.srcDB, opts.destDB),
requestStream(true),

@@ -257,3 +258,3 @@ createLinkObj()

if (srcUID) { stream.write(srcUID); stream.end() }
if (opts.srcUID) { stream.write(opts.srcUID); stream.end() }
if (cb) { stream.on('data', cb) } else { return stream }

@@ -311,4 +312,4 @@ }

// ## Property link (Plink)
// Similar to Link but taked the srcID from a property of the Streamed object
// and attached the result to a property with the name of the destination DB.
// Similar to Link but takes the srcID from a property of the Streamed object
// and attaches the result to a property with the name of the destination DB.
//

@@ -321,4 +322,7 @@ // ncbi.search('genome', 'arthropoda')

insight.track('ncbi', 'plink')
var srcDB = property.split('.').pop()
var destProperty = destDB + 'id'
var opts = typeof property === 'string' ? { property, destDB } : property
var srcDB = opts.property.split('.').pop()
var destProperty = opts.destDB + 'id'
var stream = through.obj(transform)

@@ -329,3 +333,3 @@ return stream

var self = this
var id = tool.getValue(obj, property + 'id')
var id = tool.getValue(obj, opts.property + 'id')
if (!id) {

@@ -336,3 +340,3 @@ self.push(obj)

if (!obj[destProperty]) { obj[destProperty] = [] }
ncbi.link(srcDB, destDB, id, gotData)
ncbi.link(srcDB, opts.destDB, id, gotData)
function gotData (data) {

@@ -364,7 +368,11 @@ if (data.destUIDs) { obj[destProperty] = data.destUIDs }

insight.track('ncbi', 'download')
var opts = typeof db === 'string' ? { db: db, term } : db
opts.db = opts.db
var stream = pumpify.obj(
ncbi.urls(db),
download(db)
ncbi.urls(opts.db),
download(opts)
)
if (term) { stream.write(term); stream.end() }
if (opts.term) { stream.write(opts.term); stream.end() }
if (cb) { stream.pipe(concat(cb)) } else { return stream }

@@ -393,4 +401,8 @@ }

}
var url = extractFiles[db]()
// added opts.db definition here since it is a local variable in ncbi.urls
var opts = typeof db === 'string' ? { db } : db
var url = extractFiles[opts.db]()
var path = folder + url.replace(/.*\//, '')

@@ -408,3 +420,13 @@

debug('downloading', url)
var options = { dir: folder, resume: true }
var options
if (opts.pretty === true) {
if (fs.existsSync(path)) {
console.log('File already exists in: ' + path + '\n')
options = { dir: folder, resume: true, quiet: true }
} else {
options = { dir: folder, resume: true, quiet: false }
}
} else {
options = { dir: folder, resume: true, quiet: true }
}
var dld = nugget(PROXY + url, options, function (err) {

@@ -422,3 +444,5 @@ if (err) return self.destroy(err)

})
dld.on('progress', logging)
if (opts.pretty !== true) {
dld.on('progress', logging)
}
}

@@ -449,3 +473,3 @@

insight.track('ncbi', 'urls')
var opts = typeof db === 'string' ? { db: db } : db
var opts = typeof db === 'string' ? { db } : db
cb = typeof term === 'function' ? term : cb

@@ -497,4 +521,6 @@ var extractFiles = ['gff', 'gpff', 'fasta', 'fna', 'faa', 'repeats']

var ftpArray = Array.isArray(ftpPath) ? ftpPath : [ ftpPath ]
var httpRoot = ftpArray[0]._.replace('ftp://', 'http://') // NCBI seems to return GenBank and RefSeq accessions for the same thing. We only need one.
var httpRoot = httpRoot.split('/').slice(0, -1).join('/')
// NCBI seems to return GenBank and RefSeq accessions for the same thing. We only need one.
var httpRoot = ftpArray[0]._
.replace('ftp://', 'http://')
.split('/').slice(0, -1).join('/')
request({ uri: PROXY + httpRoot, withCredentials: false }, gotFTPDir)

@@ -515,3 +541,3 @@ } else { return next() }

var basename = path.basename(httpRoot)
var fileNameProperties = base.replace(new RegExp('.*'+basename+'_'), '')
var fileNameProperties = base.replace(new RegExp('.*' + basename + '_'), '')
var fileNameExtensions = fileNameProperties.split('.')

@@ -541,12 +567,17 @@ var fileType = fileNameExtensions[0]

function get () {
if (self.tries > 20) { console.warn('try ' + self.tries + obj) }
if (self.tries > 9) {
self.emit('error', new Error(
`Query failed after ${self.tries} tries, maybe a term or network issue?
This is what failed: ${obj}`)
)
}
request({ uri: obj, json: true, timeout: timeout, withCredentials: false }, gotData)
function gotData (err, res, body) {
if (err
|| !res
|| res.statusCode !== 200
|| !body
|| (body.esearchresult && body.esearchresult.ERROR)
|| (body.esummaryresult && body.esummaryresult[0] === 'Unable to obtain query #1')
|| body.error
if (err ||
!res ||
res.statusCode !== 200 ||
!body ||
(body.esearchresult && body.esearchresult.ERROR) ||
(body.esummaryresult && body.esummaryresult[0] === 'Unable to obtain query #1') ||
body.error
) {

@@ -576,4 +607,5 @@ self.tries++

insight.track('ncbi', 'expand')
destProperty = destProperty || property
var db = property.split('.').pop()
var opts = typeof property === 'string' ? { property, destProperty } : property
opts.destProperty = opts.destProperty || opts.property
var db = opts.property.split('.').pop()
if (db === 'tax') { db = 'taxonomy' }

@@ -586,3 +618,3 @@

var self = this
var ids = tool.getValue(obj, property + 'id')
var ids = tool.getValue(obj, opts.property + 'id')
if (!ids) {

@@ -611,3 +643,3 @@ self.push(obj)

if (err) { throw new Error(err) }
obj[destProperty] = data
obj[opts.destProperty] = data
self.push(obj)

@@ -614,0 +646,0 @@ next()

81

package.json
{
"name": "bionode-ncbi",
"description": "Node.js module for working with the NCBI API (aka e-utils) using Streams.",
"version": "1.7.0",
"version": "2.0.0",
"homepage": "http://github.com/bionode/bionode-ncbi",

@@ -15,32 +15,32 @@ "repository": {

"dependencies": {
"JSONStream": "^0.10.0",
"async": "^0.9.0",
"bionode-fasta": "^0.5.3",
"cheerio": "^0.19.0",
"concat-stream": "~1.4.8",
"debug": "^2.1.3",
"JSONStream": "^1.3.1",
"async": "^2.3.0",
"bionode-fasta": "^0.5.6",
"cheerio": "^0.22.0",
"concat-stream": "~1.6.0",
"debug": "^2.6.4",
"insight": "^0.8.4",
"minimist": "^1.1.1",
"mkdirp": "^0.5.0",
"nugget": "^1.4.1",
"pumpify": "^1.3.3",
"request": "^2.55.0",
"split2": "^2.0.1",
"through2": "^0.6.3",
"mkdirp": "^0.5.1",
"nugget": "^2.0.1",
"pumpify": "^1.3.5",
"request": "^2.81.0",
"split2": "^2.1.1",
"through2": "^2.0.3",
"tool-stream": "0.2.1",
"xml2js": "^0.4.6"
"xml2js": "^0.4.17",
"yargs": "^7.1.0"
},
"devDependencies": {
"standard": "^3.3.2",
"dependency-check": "^2.3.1",
"browserify": "^9.0.7",
"browserify": "^14.3.0",
"contributor": "~0.1.25",
"coveralls": "~2.11.2",
"coveralls": "~2.13.0",
"dependency-check": "^2.8.0",
"docco": "~0.7.0",
"istanbul": "~0.3.13",
"tap-spec": "^3.0.0",
"tape": "^4.0.0",
"istanbul": "~0.4.5",
"standard": "^10.0.2",
"tap-spec": "^4.1.1",
"tape": "^4.6.3",
"tape-nock": "^1.6.0",
"testling": "^1.7.1",
"uglify-js": "^2.4.19",
"nock": "2.11.0"
"uglify-js": "^2.8.22"
},

@@ -64,3 +64,3 @@ "keywords": [

"scripts": {
"test": "standard && dependency-check . && node test/*.js | tap-spec && rm -rf ./503988",
"test": "standard && dependency-check . && node test/*.js | tap-spec",
"test-browser": "browserify test/*.js -d | testling -x 'open -a \"Google Chrome\"' | tap-spec",

@@ -72,32 +72,3 @@ "coverage": "standard && dependency-check . && istanbul cover test/bionode-ncbi.js --report lcovonly -- | tap-spec && rm -rf ./coverage",

},
"license": "MIT",
"contributors": [
{
"name": "Filip Tér",
"email": null,
"url": "https://github.com/terfn",
"contributions": 7,
"additions": 444,
"deletions": 195,
"hireable": null
},
{
"name": "Bruno Vieira",
"email": "mail@bmpvieira.com",
"url": "https://github.com/bmpvieira",
"contributions": 110,
"additions": 4818,
"deletions": 1929,
"hireable": null
},
{
"name": "=^._.^=",
"email": null,
"url": "https://github.com/maxogden",
"contributions": 7,
"additions": 84,
"deletions": 61,
"hireable": null
}
]
"license": "MIT"
}

126

README.md

@@ -8,107 +8,67 @@ <p align="center">

</p>
# bionode-ncbi
> Node.js module for working with the NCBI API (aka e-utils).
[![NPM](https://nodei.co/npm/bionode-ncbi.png?downloads=true&downloadRank=true&stars=true)](https://nodei.co/npm/bionode-ncbi/)
> Node.js module to get data from the NCBI API (aka e-utils)
[![NPM version][npm-image]][npm-url]
[![Build Status][travis-image]][travis-url]
[![Coveralls Status][coveralls-image]][coveralls-url]
[![Dependency Status][depstat-image]][depstat-url]
[![Standard style][js-standard-style-image]][js-standard-style-url]
[![Gitter chat][gitter-image]][gitter-url]
[![DOI][doi-image]][doi-url]
[![Stories in Ready at waffle.io][waffle-image]][waffle-url]
[![npm](https://img.shields.io/npm/v/bionode-ncbi.svg?style=flat-square)](http://npmjs.org/package/bionode-ncbi)
[![Travis](https://img.shields.io/travis/bionode/bionode-ncbi.svg?style=flat-square)](https://travis-ci.org/bionode/bionode-ncbi)
[![Coveralls](https://img.shields.io/coveralls/bionode/bionode-ncbi.svg?style=flat-square)](http://coveralls.io/r/bionode/bionode-ncbi)
[![Dependencies](http://img.shields.io/david/bionode/bionode-ncbi.svg?style=flat-square)](http://david-dm.org/bionode/bionode-ncbi)
[![npm](https://img.shields.io/npm/dt/bionode-ncbi.svg?style=flat-square)](https://www.npmjs.com/package/bionode-ncbi)
[![Gitter](https://img.shields.io/gitter/room/nwjs/nw.js.svg?style=flat-square)](https://gitter.im/bionode/bionode-ncbi)
[![Cite](http://img.shields.io/badge/doi-10.5281/zenodo.11315-blue.svg?style=flat-square)](http://dx.doi.org/10.5281/zenodo.11315)
Install
-------
## Install
Install ```bionode-ncbi``` with [npm](//npmjs.org):
You need to install the latest Node.JS first, please check [nodejs.org](http://nodejs.org) or do the following:
```sh
$ npm install bionode-ncbi
```bash
# Ubuntu
sudo apt-get install npm
# Mac
brew install node
# Both
npm install -g n
n stable
```
To use it as a command line tool, you can install it globally by adding ```-g``` .
To use `bionode-ncbi` as a command line tool, you can install it globally with `-g`.
Usage
-----
If you are using ```bionode-ncbi``` with Node.js, you can require the module:
```js
var ncbi = require('bionode-ncbi')
ncbi.search('sra', 'solenopsis').on('data', console.log)
```bash
npm install bionode-ncbi -g
```
Please read the [documentation](http://rawgit.com/bionode/bionode-ncbi/master/docs/bionode-ncbi.html) for the methods exposed by bionode.
Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the `node_modules` directory by doing the same command **without** `-g`.
### Command line examples
```sh
$ bionode-ncbi search taxonomy solenopsis
$ bionode-ncbi search sra human --limit 10 # or just -l
$ bionode-ncbi download assembly solenopsis invicta
$ bionode-ncbi urls sra solenopsis invicta
$ bionode-ncbi link assembly bioproject 244018
```bash
npm i bionode-ncbi # 'i' can be used as shorcut to 'install'
```
## Documentation
### Usage with [Dat](http://dat-data.com)
```sh
bionode-ncbi search gds solenopsis | dat import --json
```
Check our documentation at [doc.bionode.io](http://doc.bionode.io) or do:
Contributing
------------
To contribute, clone this repo locally and commit your code on a separate branch.
Please write unit tests for your code, and check that everything works by running the following before opening a pull-request:
```sh
$ npm test
```bash
bionode-ncbi --help
```
Please also check for code coverage:
## Contributing
We welcome all kinds of contributions at all levels of experience, please read the [CONTRIBUTING.md](CONTRIBUTING.md) to get started!
```sh
$ npm run coverage
```
## Communication channels
To rebuild the documentation using the comments in the code:
Don't be shy! Come talk to us :smiley:
```sh
$ npm run build-docs
```
Check the [issues](http://github.com/bionode/bionode-ncbi/issues) for ways to contribute.
* **Email** [mail@bionode.io](mailto:mail@bionode.io)
* **Chat room** [http://gitter.im/bionode/bionode-ncbi](http://gitter.im/bionode/bionode-ncbi)
* **IRC** #bionode on Freenode
* **Twitter** [@bionode](http://twitter.com/@bionode)
### Contributors
Please see the file [contributors.md](contributors.md) for a list.
Contacts
--------
Bruno Vieira <[mail@bmpvieira.com](mailto:mail@bmpvieira.com)> [@bmpvieira](//twitter.com/bmpvieira)
## Acknowledgements
We would like to thank all the people and institutions listed below!
Yannick Wurm ([yannick.poulet.org](http://yannick.poulet.org)) [@yannick__](//twitter.com/yannick__)
Licenses
--------
bionode-ncbi is licensed under the [MIT](https://raw.github.com/bionode/bionode-ncbi/master/LICENSE) license.
Check [ChooseALicense.com](http://choosealicense.com/licenses/mit) for details.
[npm-url]: http://npmjs.org/package/bionode-ncbi
[npm-image]: http://img.shields.io/npm/v/bionode-ncbi.svg?style=flat-square
[travis-url]: http:////travis-ci.org/bionode/bionode-ncbi
[travis-image]: http://img.shields.io/travis/bionode/bionode-ncbi.svg?style=flat-square
[coveralls-url]: http:////coveralls.io/r/bionode/bionode-ncbi
[coveralls-image]: http://img.shields.io/coveralls/bionode/bionode-ncbi.svg?style=flat-square
[depstat-url]: http://david-dm.org/bionode/bionode-ncbi
[depstat-image]: http://img.shields.io/david/bionode/bionode-ncbi.svg?style=flat-square
[js-standard-style-url]: https://github.com/feross/standard
[js-standard-style-image]: https://img.shields.io/badge/code%20style-standard-brightgreen.svg?style=flat-square
[gitter-image]: http://img.shields.io/badge/gitter-bionode/bionode--ncbi-brightgreen.svg?style=flat-square
[gitter-url]: https://gitter.im/bionode/bionode-ncbi
[waffle-image]: https://badge.waffle.io/bionode/bionode-ncbi.png?label=ready&title=issues%20ready
[waffle-url]: https://waffle.io/bionode/bionode-ncbi
[doi-url]: http://dx.doi.org/10.5281/zenodo.11315
[doi-image]: http://img.shields.io/badge/doi-10.5281/zenodo.11315-blue.svg?style=flat-square
* [graphs/contributors](https://github.com/bionode/bionode-ncbi/graphs/contributors)
* [bionode/people](https://github.com/orgs/bionode/people)
* [WurmLab](http://wurmlab.github.io)
* [Mozilla Science Lab](https://science.mozilla.org)

39

test/bionode-ncbi.js
var fs = require('fs')
var crypto = require('crypto')
var test = require('tape')
var nock = require('nock')
var tape = require('tape')
var tapeNock = require('tape-nock')
var test = tapeNock(tape)
var nock = test.nock

@@ -12,3 +14,3 @@ var ncbi = require('../')

test('Download list', function (t) {
test('Download list for assembly', function (t) {
var msg = 'should take a database name (assembly) and search term (Guillardia theta), and list datasets URLs'

@@ -26,3 +28,3 @@ var db = 'assembly'

test('Download list', function (t) {
test('Download list for sra', function (t) {
var msg = 'should take a database name (sra) and search term (Guillardia theta), and list datasets URLs'

@@ -43,3 +45,3 @@ var db = 'sra'

var path = ''
var stream = ncbi.download('assembly', 'Guillardia theta')
var stream = ncbi.download('assembly', 'ASM1036v1')
stream.on('data', function (data) { path = data.path })

@@ -52,3 +54,3 @@ stream.on('end', function () {

var sha1 = shasum.digest('hex')
var hash = 'a2dc7b3b0ae6f40d5205c4394c2fe8bc65d52bc2'
var hash = testData['sra-sha1']
t.equal(sha1, hash, msg)

@@ -60,6 +62,6 @@ setTimeout(t.end, 2000)

test('Download', function (t) {
test('Download unless file exists', function (t) {
var msg = 'repeat same download to cover already downloaded branch'
var path = ''
var stream = ncbi.download('assembly', 'Guillardia theta')
var stream = ncbi.download('assembly', 'ASM1036v1')
stream.on('data', function (data) { path = data.path })

@@ -72,3 +74,3 @@ stream.on('end', function () {

var sha1 = shasum.digest('hex')
var hash = 'a2dc7b3b0ae6f40d5205c4394c2fe8bc65d52bc2'
var hash = testData['sra-sha1']
t.equal(sha1, hash, msg)

@@ -80,3 +82,3 @@ setTimeout(t.end, 2000)

test('Search', function (t) {
test('Search assembly', function (t) {
var results1 = []

@@ -92,3 +94,3 @@ var stream = ncbi.search('assembly', 'Guillardia theta')

test('Search', function (t) {
test('Search sra', function (t) {
var results2 = []

@@ -104,3 +106,3 @@ var stream = ncbi.search('sra', 'Guillardia theta')

test('Search', function (t) {
test('Search sra with limit to one', function (t) {
var results3 = []

@@ -123,3 +125,3 @@ var stream = ncbi.search({ db: 'sra', term: 'Guillardia theta', limit: 1 })

test('Link', function (t) {
test('Link sra to bioproject', function (t) {
var results = []

@@ -135,3 +137,3 @@ var stream = ncbi.link('sra', 'bioproject', '35533')

test('Link', function (t) {
test('Link bioproject to assembly', function (t) {
var results = []

@@ -159,6 +161,6 @@ var stream = ncbi.link('bioproject', 'assembly', '53577')

test('Error Handling', function (t) {
var base = 'http://eutils.ncbi.nlm.nih.gov',
path = '/entrez/eutils/esearch.fcgi?&retmode=json&version=2.0&db=assembly&term=Guillardia_theta&usehistory=y',
results = [],
msg = 'Should detect invalid return object and throw an error stating so, showing request URL'
var base = 'http://eutils.ncbi.nlm.nih.gov'
var path = '/entrez/eutils/esearch.fcgi?&retmode=json&version=2.0&db=assembly&term=Guillardia_theta&usehistory=y'
var results = []
var msg = 'Should detect invalid return object and throw an error stating so, showing request URL'

@@ -179,2 +181,1 @@ nock(base)

})

295

test/data.json
{
"assembly": {
"guillardia-theta": {
"search": {
"uid":"503988",
"rsuid":"1011608",
"gbuid":"503988",
"assemblyaccession":"GCF_000315625.1",
"lastmajorreleaseaccession":"GCF_000315625.1",
"chainid":"315625",
"assemblyname":"Guith1",
"ucscname":"",
"ensemblname":"",
"taxid":"905079",
"organism":"Guillardia theta CCMP2712 (cryptomonads)",
"speciestaxid":"55529",
"speciesname":"Guillardia theta",
"assemblytype":"haploid",
"assemblyclass":"haploid",
"assemblystatus":"Scaffold",
"wgs":"AEIE01",
"gb_bioprojects":[
"search":{
"uid": "503988",
"rsuid": "1011608",
"gbuid": "503988",
"assemblyaccession": "GCF_000315625.1",
"lastmajorreleaseaccession": "GCF_000315625.1",
"chainid": "315625",
"assemblyname": "Guith1",
"ucscname": "",
"ensemblname": "",
"taxid": "905079",
"organism": "Guillardia theta CCMP2712 (cryptomonads)",
"speciestaxid": "55529",
"speciesname": "Guillardia theta",
"assemblytype": "haploid",
"assemblyclass": "haploid",
"assemblystatus": "Scaffold",
"wgs": "AEIE01",
"gb_bioprojects": [
{
"bioprojectaccn":"PRJNA53577",
"bioprojectid":53577
"bioprojectaccn": "PRJNA53577",
"bioprojectid": 53577
}
],
"gb_projects":[
"gb_projects": [
"53577"
],
"rs_bioprojects":[
"rs_bioprojects": [
{
"bioprojectaccn":"PRJNA223305",
"bioprojectid":223305
"bioprojectaccn": "PRJNA223305",
"bioprojectid": 223305
}
],
"rs_projects":[
"rs_projects": [
"223305"
],
"biosampleaccn":"SAMN00116900",
"biosampleid":"116900",
"biosource":{
"infraspecieslist":[
"biosampleaccn": "SAMN00116900",
"biosampleid": "116900",
"biosource": {
"infraspecieslist": [
{
"sub_type":"strain",
"sub_value":"CCMP2712"
"sub_type": "strain",
"sub_value": "CCMP2712"
}
],
"sex":"",
"isolate":""
"sex": "",
"isolate": ""
},
"coverage":"0",
"partialgenomerepresentation":"false",
"primary":"1011598",
"assemblydescription":"",
"releaselevel":"Major",
"asmreleasedate":"2012/12/06 00:00",
"seqreleasedate":"2012/12/05 00:00",
"asmupdatedate":"2014/04/22 00:00",
"ncbireleasedate":"2012/12/06 00:00",
"submissiondate":"2012/12/05 00:00",
"lastupdatedate":"2014/04/22 00:00",
"submitterorganization":"JGI",
"refseq_category":"representative genome",
"anomalouslist":[
],
"propertylist":[
"coverage": "23.66",
"partialgenomerepresentation": "false",
"primary": "1011598",
"assemblydescription": "",
"releaselevel": "Major",
"asmreleasedate_genbank": "2012/12/06 00:00",
"asmreleasedate_refseq": "2014/04/22 00:00",
"seqreleasedate": "2012/12/05 00:00",
"asmupdatedate": "2014/04/22 00:00",
"submissiondate": "2012/12/05 00:00",
"lastupdatedate": "2014/04/22 00:00",
"submitterorganization": "JGI",
"refseq_category": "representative genome",
"anomalouslist": [],
"exclfromrefseq": [],
"propertylist": [
"full-genome-representation",

@@ -76,85 +75,91 @@ "latest",

],
"synonym":{
"genbank":"GCA_000315625.1",
"refseq":"GCF_000315625.1",
"similarity":"identical"
"fromtype": "",
"synonym": {
"genbank": "GCA_000315625.1",
"refseq": "GCF_000315625.1",
"similarity": "identical"
},
"sortorder":"2C50003156259898",
"meta":{
"Stats":{
"Stat":[
"ftppath_genbank": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/315/625/GCA_000315625.1_Guith1",
"ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1",
"ftppath_assembly_rpt": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_assembly_report.txt",
"ftppath_stats_rpt": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_assembly_stats.txt",
"ftppath_regions_rpt": "",
"sortorder": "2C50003156259898",
"meta": {
"Stats": {
"Stat": [
{
"category":"alt_loci_count",
"sequence_tag":"all",
"_":"0"
"_": "0",
"category": "alt_loci_count",
"sequence_tag": "all"
},
{
"category":"chromosome_count",
"sequence_tag":"all",
"_":"0"
"_": "0",
"category": "chromosome_count",
"sequence_tag": "all"
},
{
"category":"contig_count",
"sequence_tag":"all",
"_":"5126"
"_": "5126",
"category": "contig_count",
"sequence_tag": "all"
},
{
"category":"contig_l50",
"sequence_tag":"all",
"_":"587"
"_": "587",
"category": "contig_l50",
"sequence_tag": "all"
},
{
"category":"contig_n50",
"sequence_tag":"all",
"_":"40445"
"_": "40445",
"category": "contig_n50",
"sequence_tag": "all"
},
{
"category":"non_chromosome_replicon_count",
"sequence_tag":"all",
"_":"0"
"_": "0",
"category": "non_chromosome_replicon_count",
"sequence_tag": "all"
},
{
"category":"replicon_count",
"sequence_tag":"all",
"_":"0"
"_": "0",
"category": "replicon_count",
"sequence_tag": "all"
},
{
"category":"scaffold_count",
"sequence_tag":"all",
"_":"669"
"_": "669",
"category": "scaffold_count",
"sequence_tag": "all"
},
{
"category":"scaffold_count",
"sequence_tag":"placed",
"_":"0"
"_": "0",
"category": "scaffold_count",
"sequence_tag": "placed"
},
{
"category":"scaffold_count",
"sequence_tag":"unlocalized",
"_":"0"
"_": "0",
"category": "scaffold_count",
"sequence_tag": "unlocalized"
},
{
"category":"scaffold_count",
"sequence_tag":"unplaced",
"_":"669"
"_": "669",
"category": "scaffold_count",
"sequence_tag": "unplaced"
},
{
"category":"scaffold_l50",
"sequence_tag":"all",
"_":"52"
"_": "52",
"category": "scaffold_l50",
"sequence_tag": "all"
},
{
"category":"scaffold_n50",
"sequence_tag":"all",
"_":"545808"
"_": "545808",
"category": "scaffold_n50",
"sequence_tag": "all"
},
{
"category":"total_length",
"sequence_tag":"all",
"_":"87145349"
"_": "87145349",
"category": "total_length",
"sequence_tag": "all"
},
{
"category":"ungapped_length",
"sequence_tag":"all",
"_":"83457412"
"_": "83457412",
"category": "ungapped_length",
"sequence_tag": "all"
}

@@ -166,8 +171,16 @@ ]

{
"type": "GenBank",
"_": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1"
"_": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_assembly_report.txt",
"type": "Assembly_rpt"
},
{
"type": "RefSeq",
"_": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000315625.1_Guith1"
"_": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/315/625/GCA_000315625.1_Guith1",
"type": "GenBank"
},
{
"_": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1",
"type": "RefSeq"
},
{
"_": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_assembly_stats.txt",
"type": "Stats_rpt"
}

@@ -183,36 +196,49 @@ ]

"urls": {
"uid" : "503988",
"stats" : {
"txt" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_assembly_stats.txt"
"uid": "503988",
"assembly_structure": {
"dir": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_assembly_structure/"
},
"protein" : {
"gpff" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_protein.gpff.gz",
"faa" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_protein.faa.gz"
"assembly_report": {
"txt": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_assembly_report.txt"
},
"rm" : {
"out" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_rm.out.gz",
"run" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_rm.run"
"assembly_stats": {
"txt": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_assembly_stats.txt"
},
"report" : {
"txt" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_assembly_report.txt"
"cds_from_genomic": {
"fna": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_cds_from_genomic.fna.gz"
},
"structure" : {
"dir" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_assembly_structure/"
"feature_table": {
"txt": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_feature_table.txt.gz"
},
"md5checksums" : {
"txt" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/md5checksums.txt"
"genomic": {
"fna": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_genomic.fna.gz",
"gbff": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_genomic.gbff.gz",
"gff": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_genomic.gff.gz"
},
"genomic" : {
"gbff" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_genomic.gbff.gz",
"gff" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_genomic.gff.gz",
"fna" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_genomic.fna.gz"
"protein": {
"faa": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_protein.faa.gz",
"gpff": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_protein.gpff.gz"
},
"README" : {
"txt" : "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/README.txt"
"rm": {
"out": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_rm.out.gz",
"run": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_rm.run"
},
"table": {
"txt": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_feature_table.txt.gz"
"rna": {
"fna": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_rna.fna.gz",
"gbff": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_rna.gbff.gz"
},
"wgsmaster": {
"gbff": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000315625.1_Guith1/GCA_000315625.1_Guith1_wgsmaster.gbff.gz"
"rna_from_genomic": {
"fna": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/GCF_000315625.1_Guith1_rna_from_genomic.fna.gz"
},
"README": {
"txt": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/README.txt"
},
"annotation_hashes": {
"txt": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/annotation_hashes.txt"
},
"assembly_status": {
"txt": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/assembly_status.txt"
},
"md5checksums": {
"txt": "http://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/315/625/GCF_000315625.1_Guith1/md5checksums.txt"
}

@@ -265,3 +291,4 @@ }

"message" : "NCBI returned invalid results, this could be a temporary issue with NCBI servers.\nRequest URL: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?&retmode=json&version=2.0&db=assembly&term=Guillardia_theta&usehistory=y"
}
},
"sra-sha1": "0b38d7bb2ee9cbfb575a07ff5e2c243a3f129d8d"
}

26

test/guillardia-theta.sra.json
[
{"uid":"35523","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"19695","total_bases":"5631540","total_size":"13923541","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029662","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070672","total_spots":"19695","total_bases":"5631540","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35524","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"204588","total_bases":"58208970","total_size":"146515335","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029663","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070673","total_spots":"204588","total_bases":"58208970","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35525","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"295457","total_bases":"85081326","total_size":"216274455","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029664","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070674","total_spots":"295457","total_bases":"85081326","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35526","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"11355","total_bases":"2962463","total_size":"7479863","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029665","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZC","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070675","total_spots":"11355","total_bases":"2962463","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35527","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"286676","total_bases":"72084130","total_size":"191124885","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029666","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZC","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070676","total_spots":"286676","total_bases":"72084130","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35528","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"971916","total_bases":"513131403","total_size":"1174625556","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029667","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070677","total_spots":"971916","total_bases":"513131403","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35529","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"1131540","total_bases":"588220300","total_size":"1327676112","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029668","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070678","total_spots":"1131540","total_bases":"588220300","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35530","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"875108","total_bases":"467593710","total_size":"1055151585","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029669","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070679","total_spots":"875108","total_bases":"467593710","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35531","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"1277503","total_bases":"657634727","total_size":"1479299694","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029670","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070680","total_spots":"1277503","total_bases":"657634727","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35532","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"873145","total_bases":"341989978","total_size":"860077955","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029671","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GPNF","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070681","total_spots":"873145","total_bases":"341989978","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35533","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"instrument_model":"454 GS FLX","_":"LS454"},"Statistics":{"total_runs":"1","total_spots":"853766","total_bases":"335390762","total_size":"847553880","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029672","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GPNF","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070682","total_spots":"853766","total_bases":"335390762","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"333627","expxml":{"Summary":{"Title":"Guillardia theta CCMP2712 Transcriptome","Platform":{"instrument_model":"Illumina HiSeq 2000","_":"ILLUMINA"},"Statistics":{"total_runs":"1","total_spots":"182747799","total_bases":"36549559800","total_size":"22708555668","load_done":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA067334","center_name":"Dalhousie University","contact_name":"Naoko Tanifuji","lab_name":"John Archibald"},"Experiment":{"acc":"SRX242847","ver":"1","status":"public","name":"Guillardia theta CCMP2712 Transcriptome"},"Study":{"acc":"SRP018737","name":"Guillardia theta CCMP2712Transcriptome or Gene expression"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS396737","name":""},"Instrument":{"ILLUMINA":"Illumina HiSeq 2000"},"Library_descriptor":{"LIBRARY_NAME":"","LIBRARY_STRATEGY":"RNA-Seq","LIBRARY_SOURCE":"TRANSCRIPTOMIC","LIBRARY_SELECTION":"cDNA","LIBRARY_LAYOUT":{"PAIRED":{"NOMINAL_LENGTH":"300"}}},"Bioproject":"SRP018737"},"runs":{"Run":[{"acc":"SRR747855","total_spots":"182747799","total_bases":"36549559800","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2014/02/19","updatedate":"2013/02/20"},
{"uid":"785981","expxml":{"Summary":{"Title":"Whole transcriptome sequencing of Guillardia theta CCMP 2712 - MMETSP0046_2","Platform":{"instrument_model":"Illumina HiSeq 2000","_":"ILLUMINA"},"Statistics":{"total_runs":"1","total_spots":"21079444","total_bases":"4215888800","total_size":"2880906452","load_done":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA166613","center_name":"NCGR","contact_name":"Kelly Schilling","lab_name":""},"Experiment":{"acc":"SRX549023","ver":"1","status":"public","name":"Whole transcriptome sequencing of Guillardia theta CCMP 2712 - MMETSP0046_2"},"Study":{"acc":"SRP042159","name":"Marine Microbial Eukaryote Transcriptome Sequencing Project"},"Organism":{"taxid":"55529","ScientificName":"Guillardia theta"},"Sample":{"acc":"SRS616861","name":""},"Instrument":{"ILLUMINA":"Illumina HiSeq 2000"},"Library_descriptor":{"LIBRARY_STRATEGY":"RNA-Seq","LIBRARY_SOURCE":"TRANSCRIPTOMIC","LIBRARY_SELECTION":"RANDOM PCR","LIBRARY_LAYOUT":{"PAIRED":""}},"Bioproject":"SRP042159"},"runs":{"Run":[{"acc":"SRR1294409","total_spots":"21079444","total_bases":"4215888800","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2015/07/22","updatedate":"2014/05/21"}
{"uid":"35523","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"19695","total_bases":"5631540","total_size":"13923541","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029662","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070672","total_spots":"19695","total_bases":"5631540","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35524","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"204588","total_bases":"58208970","total_size":"146515335","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029663","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070673","total_spots":"204588","total_bases":"58208970","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35525","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"295457","total_bases":"85081326","total_size":"216274455","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029664","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070674","total_spots":"295457","total_bases":"85081326","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35526","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"11355","total_bases":"2962463","total_size":"7479863","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029665","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZC","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070675","total_spots":"11355","total_bases":"2962463","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35527","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"286676","total_bases":"72084130","total_size":"191124885","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029666","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZC","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070676","total_spots":"286676","total_bases":"72084130","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35528","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"971916","total_bases":"513131403","total_size":"1174625556","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029667","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070677","total_spots":"971916","total_bases":"513131403","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35529","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"1131540","total_bases":"588220300","total_size":"1327676112","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029668","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070678","total_spots":"1131540","total_bases":"588220300","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35530","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"875108","total_bases":"467593710","total_size":"1055151585","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029669","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070679","total_spots":"875108","total_bases":"467593710","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35531","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"1277503","total_bases":"657634727","total_size":"1479299694","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029670","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070680","total_spots":"1277503","total_bases":"657634727","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35532","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"873145","total_bases":"341989978","total_size":"860077955","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029671","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GPNF","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070681","total_spots":"873145","total_bases":"341989978","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"35533","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"853766","total_bases":"335390762","total_size":"847553880","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029672","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GPNF","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Bioproject":"SRP004020","Biosample":"SAMN00116900"},"runs":{"Run":[{"acc":"SRR070682","total_spots":"853766","total_bases":"335390762","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2011/10/29","updatedate":"2010/10/29"},
{"uid":"333627","expxml":{"Summary":{"Title":"Guillardia theta CCMP2712 Transcriptome","Platform":{"_":"ILLUMINA","instrument_model":"Illumina HiSeq 2000"},"Statistics":{"total_runs":"1","total_spots":"182747799","total_bases":"36549559800","total_size":"22708555668","load_done":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA067334","center_name":"Dalhousie University","contact_name":"Naoko Tanifuji","lab_name":"John Archibald"},"Experiment":{"acc":"SRX242847","ver":"1","status":"public","name":"Guillardia theta CCMP2712 Transcriptome"},"Study":{"acc":"SRP018737","name":"Guillardia theta CCMP2712Transcriptome or Gene expression"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS396737","name":""},"Instrument":{"ILLUMINA":"Illumina HiSeq 2000"},"Library_descriptor":{"LIBRARY_NAME":"","LIBRARY_STRATEGY":"RNA-Seq","LIBRARY_SOURCE":"TRANSCRIPTOMIC","LIBRARY_SELECTION":"cDNA","LIBRARY_LAYOUT":{"PAIRED":{"NOMINAL_LENGTH":"300"}}},"Bioproject":"SRP018737","Biosample":"SAMN01923029"},"runs":{"Run":[{"acc":"SRR747855","total_spots":"182747799","total_bases":"36549559800","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2014/02/19","updatedate":"2013/02/20"},
{"uid":"785981","expxml":{"Summary":{"Title":"Whole transcriptome sequencing of Guillardia theta CCMP 2712 - MMETSP0046_2","Platform":{"_":"ILLUMINA","instrument_model":"Illumina HiSeq 2000"},"Statistics":{"total_runs":"1","total_spots":"21079444","total_bases":"4215888800","total_size":"2837480854","load_done":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA166613","center_name":"NCGR","contact_name":"Kelly Schilling","lab_name":""},"Experiment":{"acc":"SRX549023","ver":"1","status":"public","name":"Whole transcriptome sequencing of Guillardia theta CCMP 2712 - MMETSP0046_2"},"Study":{"acc":"SRP042159","name":"Marine Microbial Eukaryote Transcriptome Sequencing Project"},"Organism":{"taxid":"55529","ScientificName":"Guillardia theta"},"Sample":{"acc":"SRS616861","name":""},"Instrument":{"ILLUMINA":"Illumina HiSeq 2000"},"Library_descriptor":{"LIBRARY_STRATEGY":"RNA-Seq","LIBRARY_SOURCE":"TRANSCRIPTOMIC","LIBRARY_SELECTION":"RANDOM PCR","LIBRARY_LAYOUT":{"PAIRED":""}},"Bioproject":"SRP042159","Biosample":"SAMN02740393"},"runs":{"Run":[{"acc":"SRR1294409","total_spots":"21079444","total_bases":"4215888800","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":" ","createdate":"2015/07/22","updatedate":"2014/05/21"}
]
contributors.md
.npmignore

Sorry, the diff of this file is not supported yet

.travis.yml

Sorry, the diff of this file is not supported yet

docs/bionode-ncbi.html

Sorry, the diff of this file is not supported yet

test/p53-nucest.json

Sorry, the diff of this file is too big to display

SocketSocket SOC 2 Logo

Product

  • Package Alerts
  • Integrations
  • Docs
  • Pricing
  • FAQ
  • Roadmap
  • Changelog

About

Packages

npm

Go

Maven

PyPI

Rubygems

Stay in touch

Get open source security insights delivered straight into your inbox.

  • Terms
  • Privacy
  • Security

Made with ⚡️ by Socket Inc