biojs-io-gff

A GFF (general feature format) parser

Official Spec

<seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]

Short description about the formats.

Supported formats

• GFF 3
• Jalview feature format

Getting Started

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

var gff = require('biojs-io-gff');

Documentation

.read(file, cb)

Callback with parseSeqs or Promise

var p = gff.read("https://cdn.rawgit.com/greenify/biojs-io-gff/master/test/import.gff3");
// ..
p.then(function(seqs){
  // handle the model
}, function(err){
    console.warn(err);
});

.parseSeqs(str) (alias: parse)

Parameter: GFF file (as string) Type: String Example: SEQ1 EMBL atg 103 105 . + 0

Returns a dictionary of all sequences. Each sequences is an array of its features.

gff.parseSeqs('SEQ1  EMBL  atg  103  105  .  +  0');

Result

{ "seqs":
  { "SEQ1": 
        [ { seqname: 'SEQ1',
            source: 'EMBL',
            feature: 'atg',
            start: 103,
        	end: 105,
        	strand: '+',
        	frame: 0,
        	attributes: {} } ]
  },
  "config": {
    type: "gff3"
  }
}

.parseLines(str)

Parameter: GFF file Type: String Example: SEQ1 EMBL atg 103 105 . + 0

The 'parse' method converts a GFF into its JSON representation.

How to use this method

gff.parseLines('SEQ1  EMBL  atg  103  105  .  +  0');

Result

{ "features":
    [{ seqname: 'SEQ1',
    	source: 'EMBL',
    	feature: 'atg',
    	start: 103,
    	end: 105,
    	strand: '+',
    	frame: 0,
    	attributes: {} } ],
  "config": {
    type: "gff3"
  }
}

.exportLines(lines)

Return the textual GFF representation for the given lines

.exportSeqs(seqs) (alias: export)

Return the textual GFF representation for the given seqs

.parseLine(line)

Parameter: GFF line Type: String Example: SEQ1 EMBL atg 103 105 . + 0

The 'parseLine' method converts a GFF line into its JSON representation.

gff.parseLine('SEQ1  EMBL  atg  103  105  .  +  0');

Gotchas

• undefined properties (dots) are removed (checking for undefined is native)

TODO

• add option to group seqs after parent

Contributing

Please submit all issues and pull requests to the greenify/biojs-io-gff 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) 2014, greenify

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.