Merge pull request #9 from TeselaGen/aligningshortseqreads

Aligningshortseqreads
TeselaGen · May 3, 2018 · 7d7cd26 · 7d7cd26
2 parents ad9b8b8 + 9bd81e3
commit 7d7cd26
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Showing 9 changed files with 644 additions and 17 deletions.
diff --git a/src/addGapsToSeqReads.js b/src/addGapsToSeqReads.js
diff --git a/src/addGapsToSeqReads.test.js b/src/addGapsToSeqReads.test.js
diff --git a/src/deleteSequenceDataAtRange.test.js b/src/deleteSequenceDataAtRange.test.js
@@ -3,7 +3,7 @@
 // tap.mochaGlobals();
 const chai = require("chai");
 const { getRangeLength } = require("ve-range-utils");
-const {cloneDeep} = require('lodash');
+const { cloneDeep } = require("lodash");
 
 chai.should();
 const chaiSubset = require("chai-subset");
@@ -27,14 +27,16 @@ describe("deleteSequenceDataAtRange", function() {
       sequence: "atagatag",
       features: {
         "1": {
-          start: 7, end:7}
+          start: 7,
+          end: 7
+        }
       }
     };
-    const clonedExistingSeq = cloneDeep(existingSequence)
+    const clonedExistingSeq = cloneDeep(existingSequence);
     let range = { start: 3, end: 5 };
     let postDeleteSeqData = deleteSequenceDataAtRange(existingSequence, range);
-    existingSequence.should.deep.equal(clonedExistingSeq)
-    console.log('existingSequence:',existingSequence)
+    existingSequence.should.deep.equal(clonedExistingSeq);
+    // console.log('existingSequence:',existingSequence)
     postDeleteSeqData.sequence.length.should.equal(
       existingSequence.sequence.length - getRangeLength(range)
     );
@@ -61,7 +63,7 @@ describe("deleteSequenceDataAtRange", function() {
       start: 3,
       end: 7
     });
-    console.log("post:", postDeleteSeqData);
+    // console.log("post:", postDeleteSeqData);
     postDeleteSeqData.should.containSubset({
       sequence: "atgga",
       features: [{ start: 0, end: 4 }]
@@ -77,7 +79,7 @@ describe("deleteSequenceDataAtRange", function() {
       start: 3,
       end: 3
     });
-    console.log("post:", postDeleteSeqData);
+    // console.log("post:", postDeleteSeqData);
     postDeleteSeqData.should.containSubset({
       sequence: "atggagaga",
       parts: [{ start: 4, end: 8 }]

diff --git a/src/findSequenceMatches.test.js b/src/findSequenceMatches.test.js
@@ -41,11 +41,14 @@ describe("findSequenceMatches", function() {
     ]);
   });
   it("non-ambiguous, dna searches for nothing results in empty array", function() {
-    const matches = findSequenceMatches("atg", "*", { });
+    const matches = findSequenceMatches("atg", "*", {});
     expect(matches).toEqual([]);
   });
   it("ambiguous, protein searches for nothing results in empty array", function() {
-    const matches = findSequenceMatches("atg", "*", { isProteinSearch: true, isAmbiguous: true });
+    const matches = findSequenceMatches("atg", "*", {
+      isProteinSearch: true,
+      isAmbiguous: true
+    });
     expect(matches).toEqual([]);
   });
   it("ambiguous, dna searches for nothing results in empty array", function() {
@@ -69,12 +72,14 @@ describe("findSequenceMatches", function() {
   it(" AA with * as stop codon", function() {
     expect(
       findSequenceMatches("atgtaaccc", "M**", { isProteinSearch: true })
-    ).toEqual([
-    ]);
+    ).toEqual([]);
   });
   it("works with ambiguous AA", function() {
     expect(
-      findSequenceMatches("atgatg", "MX", { isProteinSearch: true, isAmbiguous: true })
+      findSequenceMatches("atgatg", "MX", {
+        isProteinSearch: true,
+        isAmbiguous: true
+      })
     ).toEqual([
       {
         start: 0,
@@ -84,7 +89,10 @@ describe("findSequenceMatches", function() {
   });
   it("works with ambiguous AA with * in search string", function() {
     expect(
-      findSequenceMatches("atgtaa", "M*", { isProteinSearch: true, isAmbiguous: true })
+      findSequenceMatches("atgtaa", "M*", {
+        isProteinSearch: true,
+        isAmbiguous: true
+      })
     ).toEqual([
       {
         start: 0,
@@ -173,10 +181,10 @@ describe("findSequenceMatches", function() {
       { bottomStrand: true, end: 2, start: 2 },
       { bottomStrand: true, end: 1, start: 1 }
     ]);
-    console.log(
-      'findSequenceMatches("atg", "n", { isAmbiguous: true }):',
-      findSequenceMatches("atg", "n", { isAmbiguous: true })
-    );
+    // console.log(
+    //   'findSequenceMatches("atg", "n", { isAmbiguous: true }):',
+    //   findSequenceMatches("atg", "n", { isAmbiguous: true })
+    // );
     expect(
       findSequenceMatches("atg", "n", {
         isAmbiguous: true,