biojs-io-newick
Version:
Parses newick strings into JSON and JSON into newick
262 lines (250 loc) • 7.69 kB
JavaScript
require=(function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);throw new Error("Cannot find module '"+o+"'")}var f=n[o]={exports:{}};t[o][0].call(f.exports,function(e){var n=t[o][1][e];return s(n?n:e)},f,f.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s})({1:[function(require,module,exports){
/**
* Extended Newick format parser in JavaScript.
*
* Copyright (c) Miguel Pignatelli 2014 based on Jason Davies
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*
* Example tree (from http://en.wikipedia.org/wiki/Newick_format):
*
* +--0.1--A
* F-----0.2-----B +-------0.3----C
* +------------------0.5-----E
* +---------0.4------D
*
* Newick format:
* (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
*
* Converted to JSON:
* {
* name: "F",
* children: [
* {name: "A", branch_length: 0.1},
* {name: "B", branch_length: 0.2},
* {
* name: "E",
* length: 0.5,
* children: [
* {name: "C", branch_length: 0.3},
* {name: "D", branch_length: 0.4}
* ]
* }
* ]
* }
*
* Converted to JSON, but with no names or lengths:
* {
* children: [
* {}, {}, {
* children: [{}, {}]
* }
* ]
* }
*/
module.exports = parse_nhx = function(s) {
var ancestors = [];
var tree = {};
// var tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
//[&&NHX:D=N:G=ENSG00000139618:T=9606]
var tokens = s.split( /\s*(;|\(|\)|\[|\]|,|:|=)\s*/ );
for (var i=0; i<tokens.length; i++) {
var token = tokens[i];
switch (token) {
case '(': // new children
var subtree = {};
tree.children = [subtree];
ancestors.push(tree);
tree = subtree;
break;
case ',': // another branch
var subtree = {};
ancestors[ancestors.length-1].children.push(subtree);
tree = subtree;
break;
case ')': // optional name next
tree = ancestors.pop();
break;
case ':': // optional length next
break;
default:
var x = tokens[i-1];
// var x2 = tokens[i-2];
if (x == ')' || x == '(' || x == ',') {
tree.name = token;
}
else if (x == ':') {
var test_type = typeof token;
if(!isNaN(token)){
tree.branch_length = parseFloat(token);
}
// tree.length = parseFloat(token);
}
else if (x == '='){
var x2 = tokens[i-2];
switch(x2){
case 'D':
tree.duplication = token;
break;
case 'G':
tree.gene_id = token;
break;
case 'T':
tree.taxon_id = token;
break;
}
}
else {
var test;
}
}
}
return tree;
};
},{}],"H99CHA":[function(require,module,exports){
module.exports = require('./newick');
module.exports.parse_nhx = require('./extended_newick');
},{"./extended_newick":1,"./newick":4}],"biojs-io-newick":[function(require,module,exports){
module.exports=require('H99CHA');
},{}],4:[function(require,module,exports){
/**
* Newick format parser in JavaScript.
*
* Copyright (c) edited by Miguel Pignatelli 2014, based on Jason Davies 2010.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*
* Example tree (from http://en.wikipedia.org/wiki/Newick_format):
*
* +--0.1--A
* F-----0.2-----B +-------0.3----C
* +------------------0.5-----E
* +---------0.4------D
*
* Newick format:
* (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
*
* Converted to JSON:
* {
* name: "F",
* children: [
* {name: "A", branch_length: 0.1},
* {name: "B", branch_length: 0.2},
* {
* name: "E",
* length: 0.5,
* children: [
* {name: "C", branch_length: 0.3},
* {name: "D", branch_length: 0.4}
* ]
* }
* ]
* }
*
* Converted to JSON, but with no names or lengths:
* {
* children: [
* {}, {}, {
* children: [{}, {}]
* }
* ]
* }
*/
module.exports.parse_newick = function (s) {
var ancestors = [];
var tree = {};
var tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
for (var i=0; i<tokens.length; i++) {
var token = tokens[i];
switch (token) {
case '(': // new children
var subtree = {};
tree.children = [subtree];
ancestors.push(tree);
tree = subtree;
break;
case ',': // another branch
var subtree = {};
ancestors[ancestors.length-1].children.push(subtree);
tree = subtree;
break;
case ')': // optional name next
tree = ancestors.pop();
break;
case ':': // optional length next
break;
default:
var x = tokens[i-1];
if (x == ')' || x == '(' || x == ',') {
tree.name = token;
} else if (x == ':') {
tree.branch_length = parseFloat(token);
}
}
}
return tree;
};
module.exports.parse_json = function (json) {
function nested(nest){
var subtree = "";
if(nest.hasOwnProperty('children')){
var children = [];
nest.children.forEach(function(child){
var subsubtree = nested(child);
children.push(subsubtree);
});
var substring = children.join();
if(nest.hasOwnProperty('name')){
subtree = "("+substring+")" + nest.name;
}
if(nest.hasOwnProperty('branch_length')){
subtree = subtree + ":"+nest.branch_length;
}
}
else{
var leaf = "";
if(nest.hasOwnProperty('name')){
leaf = nest.name;
}
if(nest.hasOwnProperty('branch_length')){
leaf = leaf + ":"+nest.branch_length;
}
subtree = subtree + leaf;
}
return subtree;
}
return nested(json) +";";
};
},{}]},{},[])