https://github.com/jmjuanes/bedjs
Manage BED files with Node.JS (Bioinformatics)
https://github.com/jmjuanes/bedjs
bed bioinformatics fasta
Last synced: 6 months ago
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Manage BED files with Node.JS (Bioinformatics)
- Host: GitHub
- URL: https://github.com/jmjuanes/bedjs
- Owner: jmjuanes
- License: mit
- Created: 2016-01-04T20:45:12.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2016-12-06T11:34:52.000Z (almost 9 years ago)
- Last Synced: 2024-08-09T01:06:25.791Z (about 1 year ago)
- Topics: bed, bioinformatics, fasta
- Language: JavaScript
- Homepage: https://www.npmjs.com/package/bedjs
- Size: 54.7 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# bedJS
[](https://www.npmjs.com/package/bedjs)
[](https://www.npmjs.com/package/bedjs)
Manage BED (Browser Extensible Data) files with Node.JS (Bioinformatics).
## Install
Use NPM to install the package:
```
npm install bedjs
```
## Overview
### About the BED file format
A BED file is a tab delimited containing one feature of interest per line. Each line must contain at least the three first fields listed below:
| KEY | Description | Type |
|-----|-------------|------|
| chromosome | Chromosome name | String |
| start | Start position of the feature | Integer |
| end | End position of the feature | Integer |
| name | Name of the line | String |
| score | Score between 0 and 1000 | Integer |
| strand | Strand of the feature ('+' or '-') | String |
| thickStart | Start position at which the feature is drawn thickly | Integer |
| thickEnd | End position at which the feature is drawn thickly | Integer |
| itemRgb | RGB value in format R,G,B | String |
| blockCount | The number of blocks (exons) in the BED line | Integer |
| blockSizes | A comma-separated list of the block sizes | String |
| blockStarts | A comma-separated list of block starts | String |
You can read more about the BED format [here](http://Mar2016.archive.ensembl.org/info/website/upload/bed.html).
### The BED object
This tool will convert each line of a BED file in one JavaScript object, where each column of the BED file will be saved with the format `key=value`. The `key` attribute will be one of the previous table.
Example of a BED file:
```
1 6579260 6579725 PLEKHG5
1 10292069 10292214 KIF1B
1 33282660 33282997 YARS
1 156084621 156085204 LMNA
```
The previous BED file converted to a BED object will be:
```javascript
[
{ chromosome: '1', start: 6579260, end: 6579725, name: 'PLEKHG5' },
{ chromosome: '1', start: 10292069, end: 10292214, name: 'KIF1B' },
{ chromosome: '1', start: 33282660, end: 33282997, name: 'YARS' },
{ chromosome: '1', start: 156084621, end: 156085204, name: 'LMNA' }
]
```
## API
Include the package in your JavaScript code using:
```javascript
var bedJS = require('bedjs');
```
### bedJS.Read(file)
Read a BED file. Returns an array with one BED object for each line of the BED file.
```javascript
var bed = bedJS.Read('example.bed');
```
### bedJS.Write(file, bed)
Save an array with BED objects to a BED file.
```javascript
bedJS.Write('newfile.bed', bed);
```
### bedJS.Collapse
A class to combine all BED objects into a new object. The following combining methods are available:
#### bedJS.Collapse.ByRegion(bed)
Combines all BED objects with overlapping features into a new BED object. This method only combines all features that have the same chromosome and the same strand.
Example of a BED object:
```javascript
[
{ "chromosome": "2", "start": 500, "end": 600, "name": "REGION1", "score": 0, "strand": "+" },
{ "chromosome": "2", "start": 550, "end": 700, "name": "REGION2", "score": 0, "strand": "+" },
{ "chromosome": "2", "start": 500, "end": 700, "name": "REGION3", "score": 0, "strand": "-" }
]
```
If now we run:
```javascript
var bed2 = bedJS.Collapse.ByRegion(bed);
```
This will return the following array:
```javascript
[
{ "chromosome": "2", "start": 500, "end": 700, "name": "REGION1,REGION2", "score": 0, "strand": "+" },
{ "chromosome": "2", "start": 500, "end": 700, "name": "REGION3", "score": 0, "strand": "-" }
]
```
#### bedJS.Collapse.ByName(bed)
Combines all BED objects that have the same feature `name`. The output object will have the minimum start position and the maximum end position of all objects combined.
Example of a BED object:
```javascript
[
{ "chromosome": "2", "start": 500, "end": 600, "name": "REGION1", "score": 0, "strand": "+" },
{ "chromosome": "2", "start": 700, "end": 800, "name": "REGION1", "score": 0, "strand": "+" },
{ "chromosome": "2", "start": 500, "end": 700, "name": "REGION2", "score": 0, "strand": "-" }
]
```
If now we run:
```javascript
var bed2 = bedJS.Collapse.ByName(bed);
```
This will return the following array:
```javascript
[
{ "chromosome": "2", "start": 500, "end": 800, "name": "REGION1", "score": 0, "strand": "+" },
{ "chromosome": "2", "start": 500, "end": 700, "name": "REGION3", "score": 0, "strand": "-" }
]
```
### bedJS.Fasta
A set of tools to work with Fasta files.
#### bedJS.Fasta.Index(file)
Create an index of your Fasta file in JSON format. This index is required if you want to use the `bedJS.Fasta.Get` function.
```javascript
bedJS.Fasta.Index('fasta_file.fa');
```
The previous command will generate a file called `fasta_file.fa.json`. Once you have created the index file, you don't need to run it again.
#### bedJS.Fasta.Get(fasta, bed, opt)
A method to extract sequences from a Fasta file using the regions delimited in your BED file or in your BED object. The inputs of this method are:
- `fasta`: the path of your fasta file where you will extract the sequence.
- `bed`: a BED object or the path to a BED file with the regions where you want to extract the sequence.
- `opt`: an object with the following keys:
- `strand`: set it to `true` if you want to extract the sequence with the same orientation defined in the BED file. Default is `false`.
This will return an array with the sequence for each BED object.
Note that you must run `bedJS.Fasta.Index` to index the Fasta file before run this function.
Example of a Fasta file:
```
test.fa:
>1
ACTGAAAAACCCGGTTTAACGTACCGG
```
Example of a bed file
```
test.bed:
1 5 10
```
If you run:
```javascript
var sequence = bedJS.Fasta.Get('test.fa', 'test.bed', { strand: false });
// -> sequence = [ { "head": "1:5-10", "sequence": "AAAAC"}]
```
## License
© [MIT LICENSE](./LICENSE) Jose M. Juanes.