1.0.0 • Published 6 years ago
clustal-omega-wrapper v1.0.0
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');
1.0.0
6 years ago