updating getAminoAcidStringFromSequenceString to have doNotExcludeAst…

…erisk option, updating toastr error logging, updating bio parser tests for u chars

CHANGELOG.md

@@ -6,6 +6,8 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
 
 #### 0.2.0
 
+- Fixed condition for removing * [`#52`](https://github.com/TeselaGen/tg-oss/pull/52)
+- Removed * aa from dna translation at the end of sequence [`#50`](https://github.com/TeselaGen/tg-oss/pull/50)
 -  export feat locs [`#45`](https://github.com/TeselaGen/tg-oss/pull/45)
 - unifying sequence filtering so filterSequenceString is always hit and… [`#31`](https://github.com/TeselaGen/tg-oss/pull/31)
 - fixed genbank file embedded in another genbank comment [`#36`](https://github.com/TeselaGen/tg-oss/pull/36)

packages/bio-parsers/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.7",
+  "version": "0.4.9",
   "type": "commonjs",
   "dependencies": {
     "@gmod/gff": "^1.2.1",

packages/bio-parsers/test/fastaToJson.test.js

@@ -165,14 +165,14 @@ ggagagguagagagagg
         isDNA: true
       }
     );
-    expect(result[0].parsedSequence.sequence[7]).toEqual("t");
+    expect(result[0].parsedSequence.sequence[7]).toEqual("u");
     const result2 = await fastaToJson(
       `>mySeq1
 GGAGAGGUAGAGAGAGG
       `,
       { isDNA: true }
     );
-    expect(result2[0].parsedSequence.sequence[7]).toEqual("T");
+    expect(result2[0].parsedSequence.sequence[7]).toEqual("U");
   });
   it("handles parseName  option correctly", async function () {
     const fastaStr = `>gb|M73307|AGMA13GT

packages/bio-parsers/test/genbankToJson.test.js

@@ -865,7 +865,7 @@ ORIGIN
     });
   });
 
-  it("will convert U base pairs to T for DNA", () => {
+  it("will not convert U base pairs to T for DNA", () => {
     const string = fs.readFileSync(
       path.join(__dirname, "./testData/genbank/genbankWithU.gb"),
       "utf8"
@@ -875,8 +875,8 @@ ORIGIN
     res.should.be.an("array");
     res[0].success.should.be.true;
     res[0].parsedSequence.features.length.should.equal(1);
+    expect(res[0].parsedSequence.sequence).toContain("u");
     expect(res[0].parsedSequence.sequence).toContain("t");
-    expect(res[0].parsedSequence.sequence).not.toContain("u");
   });
   it("will NOT convert U base pairs to T for RNA", () => {
     const string = fs.readFileSync(

packages/ove/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.3.60",
+  "version": "0.3.62",
   "main": "./src/index.js",
   "exports": {
     ".": {

packages/sequence-utils/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.13",
+  "version": "0.3.15",
   "type": "commonjs",
   "dependencies": {
     "bson-objectid": "^2.0.4",

packages/sequence-utils/src/findSequenceMatches.js

@@ -64,18 +64,22 @@ function findSequenceMatchesTopStrand(sequence, searchString, options = {}) {
   if (isProteinSearch) {
     sequencesToCheck = [
       {
-        seqToCheck: getAminoAcidStringFromSequenceString(sequenceToUse),
+        seqToCheck: getAminoAcidStringFromSequenceString(sequenceToUse, {
+          doNotExcludeAsterisk: true
+        }),
         offset: 0
       },
       {
         seqToCheck: getAminoAcidStringFromSequenceString(
-          sequenceToUse.substr(1)
+          sequenceToUse.substr(1),
+          { doNotExcludeAsterisk: true }
         ),
         offset: 1
       },
       {
         seqToCheck: getAminoAcidStringFromSequenceString(
-          sequenceToUse.substr(2)
+          sequenceToUse.substr(2),
+          { doNotExcludeAsterisk: true }
         ),
         offset: 2
       }

packages/sequence-utils/src/findSequenceMatches.test.js

@@ -1,7 +1,7 @@
 import findSequenceMatches from "./findSequenceMatches";
 
 describe("findSequenceMatches", () => {
-  it("ambiguous protein sequence with * as stop codon", () => {
+  it("ambiguous protein sequence with asterisk as stop codon", () => {
     expect(
       findSequenceMatches("mmhlrl*", "Mxxlrl*", {
         isAmbiguous: true,
@@ -29,7 +29,7 @@ describe("findSequenceMatches", () => {
       }
     ]);
   });
-  it("protein sequence with * as stop codon", () => {
+  it("protein sequence with asterisk as stop codon", () => {
     expect(
       findSequenceMatches("mmhlrl*", "mMh", {
         isProteinSequence: true /* isProteinSearch: true */
@@ -132,11 +132,11 @@ describe("findSequenceMatches", () => {
     const matches = findSequenceMatches("atg", "*", { isAmbiguous: true });
     expect(matches).toEqual([]);
   });
-  it("ambiguous, dna searches with *", () => {
+  it("ambiguous, dna searches with asterisk", () => {
     const matches = findSequenceMatches("atg", "", { isAmbiguous: true });
     expect(matches).toEqual([]);
   });
-  it(" AA with * as stop codon", () => {
+  it("AA with asterisk as stop codon in atgtaa", () => {
     expect(
       findSequenceMatches("atgtaa", "M*", { isProteinSearch: true })
     ).toEqual([
@@ -146,7 +146,7 @@ describe("findSequenceMatches", () => {
       }
     ]);
   });
-  it(" AA with * as stop codon", () => {
+  it("AA with asterisk as stop codon in atgtaaccc", () => {
     expect(
       findSequenceMatches("atgtaaccc", "M**", { isProteinSearch: true })
     ).toEqual([]);
@@ -164,7 +164,7 @@ describe("findSequenceMatches", () => {
       }
     ]);
   });
-  it("works with ambiguous AA with * in search string", () => {
+  it("works with ambiguous AA with asterisk in search string", () => {
     expect(
       findSequenceMatches("atgtaa", "M*", {
         isProteinSearch: true,

packages/sequence-utils/src/getAminoAcidStringFromSequenceString.js

@@ -1,6 +1,9 @@
 import getAminoAcidDataForEachBaseOfDna from "./getAminoAcidDataForEachBaseOfDna";
 
-export default function getAminoAcidStringFromSequenceString(sequenceString) {
+export default function getAminoAcidStringFromSequenceString(
+  sequenceString,
+  { doNotExcludeAsterisk } = {}
+) {
   const aminoAcidsPerBase = getAminoAcidDataForEachBaseOfDna(
     sequenceString,
     true
@@ -12,7 +15,11 @@ export default function getAminoAcidStringFromSequenceString(sequenceString) {
       return;
     }
     // Check if the current amino acid is the last in the sequence and is a stop codon
-    if (index >= aminoAcidsPerBase.length - 3 && aa.aminoAcid.value === '*') {
+    if (
+      !doNotExcludeAsterisk &&
+      index >= aminoAcidsPerBase.length - 3 &&
+      aa.aminoAcid.value === "*"
+    ) {
       return;
     }
     aaArray[aa.aminoAcidIndex] = aa.aminoAcid.value;

packages/ui/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ui",
-  "version": "0.3.51",
+  "version": "0.3.52",
   "main": "./src/index.js",
   "exports": {
     ".": {

packages/ui/src/toastr.js

@@ -28,14 +28,17 @@ const generateToast = intent => (message, options) => {
       updatedTimeout = ++counter;
     }
   }
-  if (window.Cypress && intent === Intent.DANGER) {
-    console.error("toastr error message: ", message);
+  if (intent === Intent.DANGER) {
+    console.error("Toastr error message: ", message);
   }
   const uniqKey = toastToUse.show(
     {
       intent,
       message,
-      timeout: options.timeout || updatedTimeout,
+      timeout:
+        options.timeout || updatedTimeout || intent === Intent.DANGER
+          ? 60000
+          : undefined,
       action: options.action,
       icon: options.icon,
       className: options.className

tools/scripts/publish.mjs

@@ -24,7 +24,7 @@ function invariant(condition, message) {
 
 // Executing publish script: node path/to/publish.mjs {name} --version {version} --tag {tag}
 // Default "tag" to "next" so we won't publish the "latest" tag by accident.
-let [, , name, version, tag = "next"] = process.argv;
+let [, , name, version, tag = "latest"] = process.argv;
 
 // Get all internal dependencies to write them to the package.json in the dist folder
 execSync(`yarn nx graph --file=output.json`);