blastutils
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1.1.15 • Public • Published

blastutils

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a BLAST+ wrapper(inspired from blastjs) for Node.js

This version of blastjs is rewritten in ts for better scalability. Additional commands like blastdb_aliasing is also added for usage.

Install

If you do not have Node.js installed you can get it at https://nodejs.org

npm install blastutils

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 = require('blastutils');
 
var type = 'nucl';
var fileIn = './test.fasta';
var outPath = './';
var name = 'example';
 
 
 
blast.makeDB(type, fileIn, outPath, name, function(err){
  if(err){
    console.error(err);   
  } else {
    console.log('database created at', outPath);
  }
});

blast n

var blast = require('blastutils');
 
blast.outputString(true); //optional, provides string output instead of JSON
 
var dbPath = './example';
var query = '>24.6jsd2.Tut\nGGTGTTGATCATGGCTCAGGACAAACGCTGGCGGCGTGCTTAATACATGCAAGTCGAACGGGCTACCTTCGGGTAGCTAGTG'
+'\n>24.6jsd3.Tut\nATGATCATGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGAAGGGGCAACTCTTT';
var dbPath = path.join(__dirname + '/example');
 
var option={
    type:"blastn",
    outputDirectory:__dirname + "/results/" ,
    rawOutput:true,
    db:path.join(__dirname + '/example'),
    outfmt:12,
    query:Nquery,
    remote:false,
    outputfileformat:"json",
    rawInput: true
}
 
var Alias={
    dblist:['example','exampleProtein'],
    dbtype:"nucl",
    out:"aliasdb",
    title:"aliasdb",
    directory:__dirname
 
}
 
 
blast.blastN(dbPath, query,option, function (err, output) {
  if(!err){
    console.log(output);
  }
});
 

API

  • .makeDB(type, fileIn, outPath, name, cb)
    callback is passed (err, stdOut, stdErr, fileOut).

  • .blastN(db, query,option, cb)
    callback is passed (err, output).

  • .blastP(db, query,option, cb)
    callback is passed (err, output).

  • .blastX(db, query,option, cb)
    callback is passed (err, output).

  • .tblastN(db, query,option, cb)
    callback is passed (err, output).

  • .tblastX(db, query,option, cb)
    callback is passed (err, output).

  • .outputString(boolean)
    this toggles the output being in a string (true) or as JSON (false).
    default is JSON.

  • .blastDbAlias(Alias,cb) Pass the Alias options based on the blastdb_alias options. For Reference check this blastdb_aliastools or type

     blastdb_aliastools -help

    callback is passed (err, stdOut, stdErr, fileOut).

Updates

Passing a fasta file directly

blast n

var fastaoption={
    type:"blastn",
    outputDirectory:path.join(__dirname ,"/results/") ,
    rawOutput:false,
    db:path.join(__dirname + '/example'),
    outfmt:12,
    query:'/home/LT/shdba/IdeaProjects/blastjs/test/fastatest.fasta',
    remote:false,
    outputfileformat:"json",
    rawInput:false
}
 
blast.blastN(dbPath, query,fastaoption, function (err, output) {
  if(!err){
    console.log(output);
  }
});
 
  • every other thing should work the same similar to other commands.

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Install

npm i blastutils

Weekly Downloads

11

Version

1.1.15

License

MIT

Unpacked Size

129 kB

Total Files

39

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Collaborators

  • sshetye