bioutils - npm Package Compare versions

Comparing version 0.1.0-alpha.1 to 0.1.0-alpha.2

package.json

 {
   "name": "bioutils",
-  "version": "0.1.0-alpha.01",
+  "version": "0.1.0-alpha.02",
   "license": "MIT",
@@ -5,0 +5,0 @@ "main": "src/bioUtils.js",

src/bioUtils.js

@@ -11,2 +11,3 @@ // io
 const newickParser = require('./parsers/newickParser');
+const nexusParser = require('./parsers/nexusParser');
 
@@ -31,2 +32,3 @@ // stats
     'newickParser': newickParser,
+    'nexusParser': nexusParser,
     'containsStopCodons': containsStopCodons,
@@ -33,0 +35,0 @@ 'numberOfSites': numberOfSites,

src/parsers/nexusParser.js

 /**
  * Converts a newick string into a bioUtils object
+ * TODO: This is currently only handling a small subset of nexus formats and data.
+ * TODO: This was written with simplicity and readability in mind; it can and should be speed up a bit though.
  * @param {string} nexusString input newick string using '\n' for line breaks
  * @param {object} metaData any metadata to be appended to the bioUtils JSON object
- * @returns {object} the bioUtils JSON object {'sequences': []],'tree': string,'metaData': {'fileType': string, (metaData param)}}
+ * @returns {object} the bioUtils JSON object {'sequences': [],'tree': string,'metaData': {'fileType': string, (metaData param)}}
  */ 
 function nexusParser(nexusString, metaData) {
-    
-    /** TODO:
     const nexusLines = nexusString.split("\n");
 
+    // 1. Parse out the sequences.
+    // 1a. Get a list of the labels
+    const taxaLabelsIndex = nexusLines.indexOf("\tTAXLABELS") + 1;
+    const taxaLabels = nexusLines[taxaLabelsIndex]
+        .slice(0, -1)
+        .trim()
+        .split(" ")
+        .map(name => name.slice(1, -1));
+    // 1b. Go through the list of labels and add the sequence character strings
+    const sequenceStartIndex = nexusLines.indexOf("MATRIX") + 1;
+    var sequences = [];
+    for (let i=0; i<taxaLabels.length; i++) {
+        const sequenceObject = {'name': taxaLabels[i], 'sequence': nexusLines[sequenceStartIndex + i].replace(';','').replace(' ','')}
+        sequences.push(sequenceObject)
+    }
+
+    // 2. Parse out the tree.
+    var tree;
+    const treeIndex = nexusLines.indexOf("BEGIN TREES;") + 1;
+    if (treeIndex == 1) {
+        tree = undefined;
+    } else {
+        const numberOfTrees = nexusLines.slice(treeIndex).indexOf("END;");
+        if (numberOfTrees >1) {
+            console.log('multiple trees not yet supported; the fist tree was used')
+        }
+        const treeLine = nexusLines[treeIndex];
+        tree = treeLine.substring(treeLine.indexOf("("));
+    }
+
+    // 3. Add the metaData
     var objectMetaData;
-    metaData ? objectMetaData = metaData : objectMetaData = {'fileType': 'newick'}
+    metaData ? objectMetaData = metaData : objectMetaData = {'fileType': 'nexus'}
 
+    // 4. Create and return the object
     const bioUtilsJson = {
-        'sequences': [],
+        'sequences': sequences,
         'tree': tree,
         'metaData': objectMetaData
     }
-
-    return bioUtilsJson
-    */
-   
-   return 'nexusParser not implemented yet'
+    return bioUtilsJson  
 }
 
 module.exports = nexusParser;

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Fixed alerts

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Improved metrics

Total package byte prevSize

1634246

increased by0.86%

Lines of code

2430

increased by1.72%

Worsened metrics

Number of low supply chain risk alerts

4

increased by33.33%

No dependency changes