Installation

With npm:

npm install @rnacanvas/dot-bracket

Usage

All exports of this package can be accessed as named imports.

// an example import
import { parseDotBracketFASTA } from '@rnacanvas/dot-bracket';

function parseDotBracketFASTA()

Parses a string in dot-bracket FASTA format (e.g., the text contents of a dot-bracket FASTA file).

// a dot-bracket FASTA string
var s = (
  '>Structure 1\n'
  + 'AAAGGGGAAAACCCCAAA\n'
  + '...((((....))))...'
);

var parsed = parseDotBracketFASTA(s);

parsed.name; // "Structure 1"
parsed.sequence; // "AAAGGGGAAAACCCCAAA"
parsed.dotBracket; // "...((((....))))..."

All common newline encodings are supported (i.e., \n, \r and \r\n).

The name line may be omitted.

var s = (
  'AAAGGGGAAAACCCCAAA\n'
  + '...((((....))))...'
);

var parsed = parseDotBracketFASTA(s);

parsed.name; // undefined
parsed.sequence; // "AAAGGGGAAAACCCCAAA"
parsed.dotBracket; // "...((((....))))..."

Any delta-G value trailing the dot-bracket notation will be omitted.

(Anything trailing the dot-bracket notation will be omitted.)

// has a delta-G value after its dot-bracket notation
var s = (
  '>Structure 1\n'
  + 'AAAGGGGAAAACCCCAAA\n'
  + '...((((....))))... (-6.90)'
);

var parsed = parseDotBracketFASTA(s);

parsed.name; // "Structure 1"
parsed.sequence; // "AAAGGGGAAAACCCCAAA"
parsed.dotBracket; // "...((((....))))..."

Dot-bracket notation may be a different length than the sequence.

// sequence is longer than dot-bracket notation
var s = (
  '>Structure 1\n'
  + 'AAAGGAAAACCCCAAA\n'
  + '...((....))..'
);

var parsed = parseDotBracketFASTA(s);

parsed.name; // "Structure 1"
parsed.sequence; // "AAAGGAAAACCCCAAA"
parsed.dotBracket; // "...((....)).."

Pseudoknot characters (e.g., [ ], { } and < >) are also allowed in dot-bracket notation.

var s = (
  '>Pseudoknots\n'
  + 'AUGCAUGCAUGCAUGCA\n'
  + '.(.).[.].{.}.<.>.'
);

var parsed = parseDotBracketFASTA(s);

parsed.name; // "Structure 1"
parsed.sequence; // "AUGCAUGCAUGCAUGCA"
parsed.dotBracket; // ".(.).[.].{.}.<.>."