gtf-nostream/README.md

utilities to read GTF data

# gtf-nostream

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Parse GTF data. This is a simplified version of
[@gmod/gtf](https://github.com/GMOD/gtf-js) for with just basic parsing and no
node.js stream module usage

## Install

    $ npm install --save gtf-nostream

## Usage

```js
const { parseStringSync } = require('gtf-nostream')
// or in ES6 (recommended)
import { parseStringSync } from 'gtf-nostream'

const fs = require('fs')

// parse a string of gtf synchronously
const stringOfGTF = fs.readFileSync('my_annotations.gtf', 'utf8')
const arrayOfThings = gtf.parseStringSync(stringOfGTF)
```

## Object format

### features

In GTF, features can have more than one location. We parse features as arrayrefs
of all the lines that share that feature's ID. Values that are `.` in the GTF
are `null` in the output.

A simple feature that's located in just one place:

```json
[
  {
    "seq_id": "ctg123",
    "source": null,
    "type": "gene",
    "start": 1000,
    "end": 9000,
    "score": null,
    "strand": "+",
    "phase": null,
    "attributes": {
      "ID": ["gene00001"],
      "Name": ["EDEN"]
    },
    "child_features": [],
    "derived_features": []
  }
]
```

A CDS called `cds00001` located in two places:

```json
[
  {
    "seq_id": "ctg123",
    "source": null,
    "type": "CDS",
    "start": 1201,
    "end": 1500,
    "score": null,
    "strand": "+",
    "phase": "0",
    "attributes": {
      "ID": ["cds00001"],
      "Parent": ["mRNA00001"]
    },
    "child_features": [],
    "derived_features": []
  },
  {
    "seq_id": "ctg123",
    "source": null,
    "type": "CDS",
    "start": 3000,
    "end": 3902,
    "score": null,
    "strand": "+",
    "phase": "0",
    "attributes": {
      "ID": ["cds00001"],
      "Parent": ["mRNA00001"]
    },
    "child_features": [],
    "derived_features": []
  }
]
```

## API

<!-- Generated by documentation.js. Update this documentation by updating the source code. -->

#### Table of Contents

- [ParseOptions](#parseoptions)
  - [disableDerivesFromReferences](#disablederivesfromreferences)
  - [encoding](#encoding)
  - [parseFeatures](#parsefeatures)
  - [parseDirectives](#parsedirectives)
  - [parseComments](#parsecomments)
  - [parseSequences](#parsesequences)
  - [parseAll](#parseall)

### ParseOptions

Parser options

#### disableDerivesFromReferences

Whether to resolve references to derives from features

Type:
[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)

#### encoding

Text encoding of the input GTF. default 'utf8'

Type: BufferEncoding

#### parseFeatures

Whether to parse features, default true

Type:
[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)

#### parseDirectives

Whether to parse directives, default false

Type:
[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)

#### parseComments

Whether to parse comments, default false

Type:
[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)

#### parseSequences

Whether to parse sequences, default true

Type:
[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)

#### parseAll

Parse all features, directives, comments, and sequences. Overrides other parsing
options. Default false.

Type:
[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)