gff
v0.1.7
Published
A GFF (general feature format) parser
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biojs-io-gff
A GFF (general feature format) parser
<seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]
Short description about the formats.
Supported formats
Getting Started
Install the module with: npm install biojs-io-gff
var gff = require('biojs-io-gff');
Documentation
.parse(file)
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.parse('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"
}
}
.parseSeqs(file)
Parameter: GFF file
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"
}
}
.exportLines(lines)
Return the textual GFF representation for the given lines
.exportSeqs(seqs)
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)
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.