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download from protein database #7

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download from protein database #7

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0c4de64
initial attempt at accessing protein sequence database
olgabot Dec 10, 2014
5853377
make sure to set printProteinURL in proteinURL
olgabot Dec 10, 2014
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19 changes: 18 additions & 1 deletion lib/bionode-ncbi.js
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Expand Up @@ -403,7 +403,8 @@ function createFTPURL(db) {
var self = this
var parseURL = {
sra: sraURL,
assembly: assemblyURL
assembly: assemblyURL,
protein: proteinURL
}

parseURL[db]()
Expand All @@ -425,6 +426,22 @@ function createFTPURL(db) {
}
}

function proteinURL(){
'http://www.ncbi.nlm.nih.gov/protein/XP_009457936.1?report=fasta&log$=seqview&format=text'
var runs = obj.runs.Run
async.eachSeries(runs, printProteinURL, next)
function printProteinURL(run, cb) {
var acc = run.acc
var runURL = [
'http://www.ncbi.nlm.nih.gov/protein/',
obj.accessionversion,
'?report=fasta&log$=seqview&format=text'
].join('')
self.push({url: runURL, uid: obj.uid})
cb()
}
}

function assemblyURL() {
if (obj.meta.FtpSites) {
var ftpPath = obj.meta.FtpSites.FtpPath
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