npm package discovery and stats viewer.

Discover Tips

  • General search

    [free text search, go nuts!]

  • Package details

    pkg:[package-name]

  • User packages

    @[username]

Sponsor

Optimize Toolset

I’ve always been into building performant and accessible sites, but lately I’ve been taking it extremely seriously. So much so that I’ve been building a tool to help me optimize and monitor the sites that I build to make sure that I’m making an attempt to offer the best experience to those who visit them. If you’re into performant, accessible and SEO friendly sites, you might like it too! You can check it out at Optimize Toolset.

About

Hi, 👋, I’m Ryan Hefner  and I built this site for me, and you! The goal of this site was to provide an easy way for me to check the stats on my npm packages, both for prioritizing issues and updates, and to give me a little kick in the pants to keep up on stuff.

As I was building it, I realized that I was actually using the tool to build the tool, and figured I might as well put this out there and hopefully others will find it to be a fast and useful way to search and browse npm packages as I have.

If you’re interested in other things I’m working on, follow me on Twitter or check out the open source projects I’ve been publishing on GitHub.

I am also working on a Twitter bot for this site to tweet the most popular, newest, random packages from npm. Please follow that account now and it will start sending out packages soon–ish.

Open Software & Tools

This site wouldn’t be possible without the immense generosity and tireless efforts from the people who make contributions to the world and share their work via open source initiatives. Thank you 🙏

© 2024 – Pkg Stats / Ryan Hefner

blast-ncbi-tools

v0.10.101

Published

NCBI blast+ wrapper for JBlast

Downloads

4

Readme

blast-ncbi-tools

Build Status

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.