dialign-wrapper v1.0.0

dialign-wrapper

A simple node module that wraps the functionalities of Dialign multiple sequence alignment program

Visit following site to learn more about it. https://bibiserv.cebitec.uni-bielefeld.de/dialign/

Install

You can install dialign-wrapper by running,

npm install dialign-wrapper

You can download Dialign executable by running,

node util/downloader.js

It will download the Dialign binary executable to util/bin folder

Usage

Align an unaligned sequence file and get output in FASTA format or ClustalW

• .alignSeqFile = function (inputFile, outFormat, callback)
  callback passed (err, data)

  const dialign = require('dialign-wrapper');
  var inputFile = 'samples/example.fasta';
  var outFormat = 'fasta';
  
  dialign.alignSeqFile(inputFile, outFormat, function(err,data){
      if(err){
          console.log(err);
      }else{
          console.log(data);
      }
  });
      

Align an unaligned input string (in FASTA format) and get output in FASTA format or ClustalW format

• .alignSeqString (input, outFormat, callback)
  callback passed (err, data)

    const dialign = require('dialign-wrapper');
    var outFormat = 'fasta';
    var input = '>test1\n' +
              'ACDEFGHIKLMNPQRSTVWY\n' +
              '>test2\n' +
              'XXXXACDEFGHIMNXXXPQR\n' +
              '>test3\n' +
              'ACDEFGHILMNXXXXXPQRS\n' +
              '>test4\n' +
              'XXXACDEFGHIKLMNPQRST';
    dialign.alignSeqString(input,outFormat,function(err,data){
        if(err){
            console.log(err);
        }else{
            console.log(data);
        }
    });

The output can be either the following two formats (set 'outFormat' to one of the following)

  *  fasta
  *  clustalW

You can specify a custom execution path where the dialign binary executable is placed

const dialign = require('dialign-wrapper');
var customExecPath = 'Downloads/bin';

dialign.setCustomLocation(customExecPath);

You can set environment varible 'DIALIGN2_DIR' pointing to the directory `dialign2_dir' in a custom location

NOTE: The pointed directory should include tp400_dna,tp400_prot, tp400_trans, BLOSUM files

const dialign = require('dialign-wrapper');
var envVariable = 'Downloads/bin/dialign_package/dialign2_dir';

dialign.setEnvironmentVar(envVariable);