blast.js
a BLAST+ wrapper for Node.js
a demo can be found at github.com/teammaclean/blastjs-demo
Install
If you do not have Node.js installed you can get it at https://nodejs.org
npm install blastjs
If Blast+ is not installed you can run:
node util/getBlast.js
and the latest version of Blast+ will be downloaded and placed in the bin folder for you.
Usage
make database
var blast = ; var type = 'nucl';var fileIn = './test.fasta';var outPath = './';var name = 'example'; blast;
blast n
var blast = ; blast; //optional, provides string output instead of JSON var dbPath = './example';var query = '>24.6jsd2.Tut\nGGTGTTGATCATGGCTCAGGACAAACGCTGGCGGCGTGCTTAATACATGCAAGTCGAACGGGCTACCTTCGGGTAGCTAGTG'+'\n>24.6jsd3.Tut\nATGATCATGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGAAGGGGCAACTCTTT'; blast;
API
-
.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.