Have ideas to improve npm?Join in the discussion! »

    clustal-omega-wrapper

    1.0.0 • Public • Published

    clustal-omega-wrapper

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

    Visit official Clustal Omega web site to learn more about it. http://www.clustal.org/omega/

    Install

    You can install clustal-omega-wrapper by running,

    npm install clustal-omega-wrapper

    You can download Clustal Omega executable by running,

    node util/downloader.js

    It will download the Clustal Omega executable to util/bin folder

    Usage

    Align an unaligned sequence file

    • .alignSeqFile (inputFile, outputFormat, callback)
      callback passed (err, stdOut, stdErr)

      var clustalOmega = require('clustalo-wrapper');
      var inputFile = 'samples/example.fasta';
      var outputType = 'fasta';
       
      clustalOmega.alignSeqFile(inputFile, outputType, function(err,stdout,stdErr){
          if(err){
              console.log(stdErr);
          }else{
              console.log(stdout);
          }
      });
          

    Align an unaligned input string of sequences of FASTA format

    • .alignSeqString (input, outputFormat, callback)
      callback passed (err, output)

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

    Align an unaligned seq file and an HMM

    • .alignSeqWithHmm (inputFile, inputHmmFile, outputFormat, callback)
      callback passed (err, output)

    Align an unaligned seq file and a profile

    • .alignSeqWithProfile (inputFile, inputProfile, outputFormat, callback)
      callback passed (err, output)

    Align two profiles

    • .alignTwoProfiles (profile1, profile2, outputFormat, callback)
      callback passed (err, output)

    The output can be in any of the following formats (set 'outputFormat' to one of the following)

      *  fasta
      *  clustal
      *  msf
      *  phylip
      *  selex
      *  stockholm
      *  vienna
    

    You can specify a custom execution path where the clustal omega executable is placed

    var clustalOmega = require('clustalo-wrapper');
    var customExecPath = 'Downloads/bin';
    var outputType = 'fasta';
     
    clustalOmega.setCustomLocation('../../Downloads');
     

    Install

    npm i clustal-omega-wrapper

    DownloadsWeekly Downloads

    2

    Version

    1.0.0

    License

    MIT

    Unpacked Size

    355 kB

    Total Files

    14

    Last publish

    Collaborators

    • avatar