blast-ncbi-tools

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.