blast-ncbi-tools
v0.10.101
Published
NCBI blast+ wrapper for JBlast
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blast-ncbi-tools
a BLAST+ wrapper for Node.js (modified to support jblast)
This project is based on https://www.npmjs.com/package/blastjs, however it has diverged to support jbconnect-hook-jblast
Install
npm install enuggetry/blast-ncbi-tools
Utilities
Install NCBI blast+ tools. The latest version of Blast+ will be downloaded and placed in the blastbin folder of approot.
./utils/blast_getBlastUtils.js
Setup blast+ utils using previously downloaded blast+ utils.
./utils/blast_setPathUtils.js <existing blast+ utils directory>
Download blast database into approot/blastdb. eg.
./utils/blast_downloadDb.js htgs (download full htgs database)
./utils/blast_downloadDb.js htgs.05 (download partial htgs database)
Setup existing database
./utils/blast_setPathDb.js /home/me/htgs/13apr08 htgs
Usage
blast n
var blast = require('blastjs');
blast.outputString(true); //optional, provides string output instead of JSON
var dbPath = './example';
var query = '>24.6jsd2.Tut\nGGTGTTGATCATGGCTCAGGACAAACGCTGGCGGCGTGCTTAATACATGCAAGTCGAACGGGCTACCTTCGGGTAGCTAGTG'
+'\n>24.6jsd3.Tut\nATGATCATGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGAAGGGGCAACTCTTT';
blast.blastN(dbPath, query, function (err, output) {
if(!err){
console.log(output);
}
});
API (much of this was not specifically maintained but may still work fine)
.makeDB(type, fileIn, outPath, name, cb)
callback is passed (err, stdOut, stdErr, fileOut)..blastN(db, query, cb)
callback is passed (err, output)..blastP(db, query, cb)
callback is passed (err, output)..blastX(db, query, cb)
callback is passed (err, output)..tblastN(db, query, cb)
callback is passed (err, output)..tblastX(db, query, cb)
callback is passed (err, output)..outputString(boolean)
this toggles the output being in a string (true) or as JSON (false).
default is JSON.