bioutils - npm Package Compare versions

Comparing version 0.1.0-alpha.0 to 0.1.0-alpha.1

package.json

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

src/bioUtils.js

@@ -12,8 +12,11 @@ // io
 
-// getInfo
-const containsStopCodons = require('./getInfo/containsStopCodons')
+// stats
+const containsStopCodons = require('./stats/containsStopCodons')
+const numberOfSites = require('./stats/numberOfSites')
+const numberOfSequences = require('./stats/numberOfSequences')
+const shannonEntropiesOfSites = require('./stats/misc/shannonEntropiesOfSites')
 
 // manipulation
 const translateToAminoAcids = require('./manipulation/translateToAminoAcids')
-const getSitesAsListOfStrings = require('./manipulation/getSitesAsListOfStrings')
+const getSitesAsListOfStrings = require('./manipulation/misc/getSitesAsListOfStrings')
 
@@ -29,4 +32,7 @@ module.exports = {
     'containsStopCodons': containsStopCodons,
+    'numberOfSites': numberOfSites,
+    'numberOfSequences': numberOfSequences,
+    'shannonEntropiesOfSites': shannonEntropiesOfSites,
     'translateToAminoAcids': translateToAminoAcids,
     'getSitesAsListOfStrings': getSitesAsListOfStrings
 }

src/io/inputData.js

@@ -11,3 +11,8 @@ const fastaParser = require("./../parsers/fastaParser");
  * @returns {object} the bioUtils JSON object {'sequences': [{'name': string, 'sequence': string}],'tree': string,'metaData': {'fileType': string, (metaData param)}}
- * @example inputData('>seq1\nact\n>seq2\natc\n(seq1,seq2);', {'fileType': 'fna', 'otherMetaData': 'this is an example'})
+ * @example 
+ * inputData('>seq1\nact\n>seq2\natc\n(seq1,seq2);', {'fileType': 'fna', 'otherMetaData': 'this is an example'})
+ * // returns {'sequences': [ {name:'seq1', sequence:'act'}, {name:'seq2', sequence:'atc'} ],
+ * //          'tree': '(seq1,seq2);',
+ * //          'metaData': {'fileType': 'fna', 'otherMetaData': 'this is an example'})
+ * //          }
  */ 
@@ -14,0 +19,0 @@ function inputData(dataString, metaData) {

src/io/writeFileSync.js

@@ -10,3 +10,3 @@ const fs = require("fs");
  * @param {string} filePath a relative or absolute file path 
- * @returns empty; This function writes a file but does not return anything. 
+ * @returns {null} This function writes a file but does not return anything. 
  */ 
@@ -13,0 +13,0 @@ function writeFileSync(dataObject, filePath, fileType) {

src/parsers/fastaParser.js

@@ -6,3 +6,2 @@ /**
  * @returns {object} the bioUtils JSON object {'sequences': [{'name': string, 'sequence': string}],'tree': undefined,'metaData': {'fileType': string, (metaData param)}}
- * @example inputData('>seq1\nact\n>seq2\natc);', {'fileType': 'fna', 'otherMetaData': 'this is an example'})
  */ 
@@ -9,0 +8,0 @@ function fastaParser(fastaString, metaData) {

src/parsers/fnaParser.js

@@ -6,3 +6,8 @@ /**
  * @returns {object} the bioUtils JSON object {'sequences': [{'name': string, 'sequence': string}],'tree': string,'metaData': {'fileType': string, (metaData param)}}
- * @example inputData('>seq1\nact\n>seq2\natc\n(seq1,seq2););', {'fileType': 'fna', 'otherMetaData': 'this is an example'})
+ * @example 
+ * inputData('>seq1\nact\n>seq2\natc\n(seq1,seq2);')
+ * // returns {'sequences': [ {'seq1': 'act'}, {'seq2': 'atc'} ],
+ * //          'tree': '(seq1,seq2);',
+ * //          'metaData': {'fileType': 'fna'})
+ * //          }
  */ 
@@ -9,0 +14,0 @@ function fnaParser(fnaString, metaData) {

src/parsers/newickParser.js

@@ -6,3 +6,2 @@ /**
  * @returns {object} the bioUtils JSON object {'sequences': []],'tree': string,'metaData': {'fileType': string, (metaData param)}}
- * @example inputData('>seq1\nact\n>seq2\natc\n(seq1,seq2););', {'fileType': 'fna', 'otherMetaData': 'this is an example'})
  */ 
@@ -9,0 +8,0 @@ function newickParser(newickString, metaData) {

src/parsers/nexusParser.js

@@ -6,3 +6,2 @@ /**
  * @returns {object} the bioUtils JSON object {'sequences': []],'tree': string,'metaData': {'fileType': string, (metaData param)}}
- * @example inputData('>seq1\nact\n>seq2\natc\n(seq1,seq2););', {'fileType': 'fna', 'otherMetaData': 'this is an example'})
  */ 
@@ -9,0 +8,0 @@ function nexusParser(nexusString, metaData) {

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Improved metrics

Total package byte prevSize

1620327

increased by0.23%

Number of package files

69

increased by23.21%

Lines of code

2389

increased by3.2%

Worsened metrics

Number of medium supply chain risk alerts

5

increased by25%

No dependency changes