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Fix bugs in parsing PhyloXML files #459

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Fix bugs in parsing PhyloXML files #459

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141fc03
Fix bug in parsing PhyloXML single-branching trees
miguel76 Apr 4, 2024
329d4d6
Fix parsing of multiple-phylogenies PhyloXML files
miguel76 Apr 4, 2024
f381407
Support PhyloXML string input
miguel76 Apr 4, 2024
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1 change: 1 addition & 0 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
"commander": "^6.2.1",
"csv-stringify": "^5.3.6",
"d3": "6",
"fast-xml-parser": "^4.3.6",
"jquery": "3",
"lodash": "^4.17.11",
"moment": "^2.29.4",
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28 changes: 24 additions & 4 deletions src/formats/phyloxml.js
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
import { XMLParser } from 'fast-xml-parser';

// Changes XML to JSON
// Modified version from here: http://davidwalsh.name/convert-xml-json
function xmlToJson(xml) {
Expand Down Expand Up @@ -46,15 +48,18 @@ var phyloxml_parser = function(xml, options) {

function parsePhyloxml(node, index) {
if (node.clade) {
if (!Array.isArray(node.clade)) {
node.clade = [node.clade];
}
node.clade.forEach(parsePhyloxml);
node.children = node.clade;
delete node.clade;
}

node.annotation = 1;
node.attribute = "0.01";
node.annotation = 1;
node.attribute = "0.01";
if (node.branch_length) {
node.attribute = node.branch_length;
node.attribute = node.branch_length;
}
if (node.taxonomy) {
node.name = node.taxonomy.scientific_name;
Expand All @@ -66,8 +71,23 @@ var phyloxml_parser = function(xml, options) {

var tree_json;

if (typeof xml === "string") {
if (DOMParser) {
const parser = new DOMParser();
xml = parser.parseFromString(xml, "text/xml");
} else {
const parser = new XMLParser();
xml = parser.parse(xml);
}
}

xml = xmlToJson(xml);
tree_json = xml.phyloxml.phylogeny.clade;
var phylogeny = xml.phyloxml.phylogeny;
if (Array.isArray(phylogeny)) {
phylogeny = phylogeny[0];
console.warn('PhyloXML files with multiple phylogenies are not currently supported. Only the first phylogeny will be loaded.')
}
tree_json = phylogeny.clade;
tree_json.name = "root";
parsePhyloxml(tree_json, 0);

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