biojs-io-xmfa

Parse Mauve/progressiveMauve XMFA files

Getting Started

Install the module with: npm install biojs-io-xmfa

var parser  = require(‘biojs-io-xmfa’);

read(url)

Parses a URL and calls your parse method with the returned body.

How to use this method

parser.read("https://cdn.rawgit.com/erasche/biojs-io-xmfa/master/test/simple.xmfa", function(err, model) {
  // model is the parsed url
});

If callback is undefined, read returns a promise.

var p = parser.read("https://cdn.rawgit.com/erasche/biojs-io-xmfa/master/test/simple.xmfa");
// ...
p.then(function(model) {
  // model is the parsed url
}, function(err){
  console.error("err happened during downloading", err);
});

parse(string)

var xmfa_file = fs.readFileSync("/path/to/my.xmfa");
var lcbs = parser.parse(xmfa_file);

Data Format

The data extracted from the XMFA file is available as an Array of LCBs. Each LCB is also an array containing all of the alignments from that LCB.

Example:

[ # This is the XMFA file
  [ # This is an LCB
    {
      start: 1,
      end: 5000,
      strand: '+',
      lcb_idx: 1,
      seq: 'ACTG...'
    },
    {
      start: 1000,
      end: 6000,
      strand: '+',
      lcb_idx: 2,
      seq: '-CGG...'
    },
  ]
]

Currently only supports reading, and not writing.

Contributing

Please submit all issues and pull requests to the erasche/biojs-io-xmfa repository!

Support

If you have any problem or suggestion please open an issue here.

License

This software is licensed under the Apache 2 license, quoted below.

Copyright (c) 2015, Eric Rasche

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.