adding a loose mode to guessIfSequenceIsDnaAndNotProtein

src/guessIfSequenceIsDnaAndNotProtein.js

@@ -1,6 +1,11 @@
-module.exports = function guessIfSequenceIsDnaAndNotProtein(seq, options = {}) {
-  const { threshold = 0.9, dnaLetters = ["G", "A", "T", "C", "U"] } = options;
+const { ambiguous_dna_letters } = require("./bioData");
 
+module.exports = function guessIfSequenceIsDnaAndNotProtein(seq, options = {}) {
+  const { threshold = 0.9, loose } = options;
+  const dnaLetters =
+    options.dnaLetters || loose
+      ? ambiguous_dna_letters.split("")
+      : ["G", "A", "T", "C", "U"];
   // Guess if the given sequence is DNA or Protein.
 
   //   It's considered DNA if more than 90% of the sequence is GATCs. The threshold
@@ -12,6 +17,7 @@ module.exports = function guessIfSequenceIsDnaAndNotProtein(seq, options = {}) {
     return acc;
   }, {});
   let count = 0;
+  if (!seq || !seq.length) return true;
   for (let index = 0; index < seq.length; index++) {
     const letter = seq[index];
     if (dnaLetterMap[letter.toUpperCase()]) {

src/guessIfSequenceIsDnaAndNotProtein.test.js

@@ -1,22 +1,34 @@
 const chai = require("chai");
 chai.should();
-const guessIfSequenceIsDnaAndNotProtein = require('./guessIfSequenceIsDnaAndNotProtein')
-describe('guessIfSequenceIsDnaAndNotProtein', function() {
-    it('should correctly guess that a DNA seq is DNA', function() {
-        guessIfSequenceIsDnaAndNotProtein("gtatacc").should.equal(true)
-    })
-    it('should correctly guess that a DNA seq with some ambiguity is a DNA', function() {
-        guessIfSequenceIsDnaAndNotProtein("gtatacctaacn").should.equal(true)
-    })
-    it('should correctly guess that a seq with lots of ambiguity is a protein', function() {
-        guessIfSequenceIsDnaAndNotProtein("gtatacybctaacn").should.equal(false)
-    })
-    it('should correctly guess that a DNA with lots of ambiguities is dna when the threshold is lower  ', function() {
-      guessIfSequenceIsDnaAndNotProtein("gtatacybctaacn", {
-          threshold: .5
-      }).should.equal(true)
-    })
-    it('should correctly guess that a DNA with lots of ambiguity is a dna when the ambiguous letter is included ', function() {
-        guessIfSequenceIsDnaAndNotProtein("gtatanccnnntaacn", {dnaLetters: ["g",'a', 't', 'c', 'n']}).should.equal(true)
-    })
-})
+const guessIfSequenceIsDnaAndNotProtein = require("./guessIfSequenceIsDnaAndNotProtein");
+describe("guessIfSequenceIsDnaAndNotProtein", function() {
+  it("should default to DNA for a length 0 sequecne", function() {
+    guessIfSequenceIsDnaAndNotProtein("").should.equal(true);
+  });
+  it("should correctly guess that a DNA seq is DNA", function() {
+    guessIfSequenceIsDnaAndNotProtein("gtatacc").should.equal(true);
+  });
+  it("should correctly guess that a DNA seq with some ambiguity is a DNA", function() {
+    guessIfSequenceIsDnaAndNotProtein("gtatacctaacn").should.equal(true);
+  });
+  it("should correctly guess that a seq with lots of ambiguity is a protein when in the default strict mode", function() {
+    guessIfSequenceIsDnaAndNotProtein("gtatacybctaacn", {
+      loose: false
+    }).should.equal(false);
+  });
+  it("should correctly guess that a seq with lots of ambiguity is dna when in the loose mode", function() {
+    guessIfSequenceIsDnaAndNotProtein("gtatacybctaacn", {
+      loose: true
+    }).should.equal(true);
+  });
+  it("should correctly guess that a DNA with lots of ambiguities is dna when the threshold is lower  ", function() {
+    guessIfSequenceIsDnaAndNotProtein("gtatacybctaacn", {
+      threshold: 0.5
+    }).should.equal(true);
+  });
+  it("should correctly guess that a DNA with lots of ambiguity is a dna when the ambiguous letter is included ", function() {
+    guessIfSequenceIsDnaAndNotProtein("gtatanccnnntaacn", {
+      dnaLetters: ["g", "a", "t", "c", "n"]
+    }).should.equal(true);
+  });
+});