@teselagen/sequence-utils 0.3.17 → 0.3.19

package/calculateTm.d.ts

@@ -1,2 +1,2 @@
-declare function _default(sequence: string, type: string, A: Double, R: Double, C: any, Na: Double): Double;
+declare function _default(sequence: any, type: any, A: any, R: any, C: any, Na: any): string | 0;
 export default _default;

package/findOrfsInPlasmid.d.ts

@@ -1 +1,11 @@
-export default function findOrfsInPlasmid(sequence: any, circular: any, minimumOrfSize: any, useAdditionalOrfStartCodons: any): Teselagen.bio.orf.ORF[];
+export default function findOrfsInPlasmid(sequence: any, circular: any, minimumOrfSize: any, useAdditionalOrfStartCodons: any): {
+    start: number;
+    end: number;
+    length: number;
+    internalStartCodonIndices: never[];
+    frame: number;
+    forward: any;
+    annotationTypePlural: string;
+    isOrf: boolean;
+    id: any;
+}[];

package/getOrfsFromSequence.d.ts

@@ -1,10 +1,20 @@
 /**
  * @private
  * Finds ORFs in a given DNA forward in a given frame.
- * @param  {Int} frame The frame to look in.
- * @param  {String}sequence The dna sequence.
- * @param  {Int} minimumOrfSize The minimum length of ORF to return.
- * @param  {boolean} forward Should we find forward facing orfs or reverse facing orfs
- * @return {Teselagen.bio.orf.ORF[]} The list of ORFs found.
+ * frame - The frame to look in.
+ * sequence - The dna sequence.
+ * minimumOrfSize - The minimum length of ORF to return.
+ * forward - Should we find forward facing orfs or reverse facing orfs
+ * return - The list of ORFs found.
  */
-export default function getOrfsFromSequence(options: any): Teselagen.bio.orf.ORF[];
+export default function getOrfsFromSequence(options: any): {
+    start: number;
+    end: number;
+    length: number;
+    internalStartCodonIndices: never[];
+    frame: number;
+    forward: any;
+    annotationTypePlural: string;
+    isOrf: boolean;
+    id: any;
+}[];

package/index.js

@@ -12326,7 +12326,7 @@ const modifiableTypes = [
 let allWarnings = [];
 let makeToast = /* @__PURE__ */ __name(() => {
   if (typeof window !== "undefined" && window.toastr && allWarnings.length) {
-    window.toastr.warning(allWarnings.join("\n"));
+    window.toastr.warning(lodashExports.uniq(allWarnings).join("\n"));
   }
   allWarnings = [];
 }, "makeToast");
@@ -13026,12 +13026,12 @@ const calcTmMethods = {
   // Monovalent salt concentration. 50mM is typical for PCR.
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
-   * @param  {String} sequence The DNA sequence to use.
-   * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-   * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-   * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-   * @return {Double} Temperature for the given sequence, in Celsius.
+   * sequence - The DNA sequence to use.
+   * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+   * A - Helix initation for deltaS. Defaults to -10.8.
+   * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * return - Temperature for the given sequence, in Celsius.
    */
   calculateTemperature: function(sequence, type, A, R, C, Na) {
     if (typeof type === "undefined") {
@@ -21541,6 +21541,8 @@ function getComplementAminoAcidStringFromSequenceString(sequenceString) {
 }
 __name(getComplementAminoAcidStringFromSequenceString, "getComplementAminoAcidStringFromSequenceString");
 function getComplementSequenceString(sequence, isRna) {
+  if (typeof sequence !== "string")
+    return "";
   let complementSeqString = "";
   const complementMap = lodashExports.merge(
     DNAComplementMap,

package/index.mjs

@@ -12324,7 +12324,7 @@ const modifiableTypes = [
 let allWarnings = [];
 let makeToast = /* @__PURE__ */ __name(() => {
   if (typeof window !== "undefined" && window.toastr && allWarnings.length) {
-    window.toastr.warning(allWarnings.join("\n"));
+    window.toastr.warning(lodashExports.uniq(allWarnings).join("\n"));
   }
   allWarnings = [];
 }, "makeToast");
@@ -13024,12 +13024,12 @@ const calcTmMethods = {
   // Monovalent salt concentration. 50mM is typical for PCR.
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
-   * @param  {String} sequence The DNA sequence to use.
-   * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-   * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-   * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-   * @return {Double} Temperature for the given sequence, in Celsius.
+   * sequence - The DNA sequence to use.
+   * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+   * A - Helix initation for deltaS. Defaults to -10.8.
+   * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * return - Temperature for the given sequence, in Celsius.
    */
   calculateTemperature: function(sequence, type, A, R, C, Na) {
     if (typeof type === "undefined") {
@@ -21539,6 +21539,8 @@ function getComplementAminoAcidStringFromSequenceString(sequenceString) {
 }
 __name(getComplementAminoAcidStringFromSequenceString, "getComplementAminoAcidStringFromSequenceString");
 function getComplementSequenceString(sequence, isRna) {
+  if (typeof sequence !== "string")
+    return "";
   let complementSeqString = "";
   const complementMap = lodashExports.merge(
     DNAComplementMap,

package/index.umd.js

@@ -12328,7 +12328,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   let allWarnings = [];
   let makeToast = /* @__PURE__ */ __name(() => {
     if (typeof window !== "undefined" && window.toastr && allWarnings.length) {
-      window.toastr.warning(allWarnings.join("\n"));
+      window.toastr.warning(lodashExports.uniq(allWarnings).join("\n"));
     }
     allWarnings = [];
   }, "makeToast");
@@ -13028,12 +13028,12 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     // Monovalent salt concentration. 50mM is typical for PCR.
     /**
      * Calculates temperature for DNA sequence using a given algorithm.
-     * @param  {String} sequence The DNA sequence to use.
-     * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-     * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-     * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-     * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-     * @return {Double} Temperature for the given sequence, in Celsius.
+     * sequence - The DNA sequence to use.
+     * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+     * A - Helix initation for deltaS. Defaults to -10.8.
+     * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+     * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+     * return - Temperature for the given sequence, in Celsius.
      */
     calculateTemperature: function(sequence, type, A, R, C, Na) {
       if (typeof type === "undefined") {
@@ -21543,6 +21543,8 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(getComplementAminoAcidStringFromSequenceString, "getComplementAminoAcidStringFromSequenceString");
   function getComplementSequenceString(sequence, isRna) {
+    if (typeof sequence !== "string")
+      return "";
     let complementSeqString = "";
     const complementMap = lodashExports.merge(
       DNAComplementMap,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.17",
+  "version": "0.3.19",
   "dependencies": {
     "@teselagen/range-utils": "0.3.7",
     "bson-objectid": "^2.0.4",

package/src/calculateTm.js

@@ -16,12 +16,12 @@ const calcTmMethods = {
 
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
-   * @param  {String} sequence The DNA sequence to use.
-   * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-   * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-   * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-   * @return {Double} Temperature for the given sequence, in Celsius.
+   * sequence - The DNA sequence to use.
+   * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+   * A - Helix initation for deltaS. Defaults to -10.8.
+   * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * return - Temperature for the given sequence, in Celsius.
    */
   calculateTemperature: function (sequence, type, A, R, C, Na) {
     if (typeof type === "undefined") {

package/src/filterSequenceString.js

@@ -9,7 +9,7 @@ let allWarnings = [];
 
 let makeToast = () => {
   if (typeof window !== "undefined" && window.toastr && allWarnings.length) {
-    window.toastr.warning(allWarnings.join("\n"));
+    window.toastr.warning(uniq(allWarnings).join("\n"));
   }
   allWarnings = [];
 };

package/src/filterSequenceString.test.js

@@ -8,23 +8,17 @@ describe("filterSequenceString", () => {
     });
     expect(str).toBe("tatuuaga");
     // expect(warnings[0]).toBe('Replaced "t" with "u" 2 times');
-    expect(warnings[0]).toBe(
-      "Invalid character(s) detected and removed: -, - "
-    );
+    expect(warnings[0]).toBe("Invalid character(s) detected and removed: - ");
   });
   it("should not convert u's to t's for isDna (default isDna=true) seqs", () => {
     const [str, warnings] = filterSequenceString("tatuuag--a", {});
     // expect(warnings[0]).toBe('Replaced "u" with "t" 2 times');
-    expect(warnings[0]).toBe(
-      "Invalid character(s) detected and removed: -, - "
-    );
+    expect(warnings[0]).toBe("Invalid character(s) detected and removed: - ");
     expect(str).toBe("tatuuaga");
   });
   it("should filter out unwanted chars", () => {
     const [str, warnings] = filterSequenceString("tatag--a");
-    expect(warnings[0]).toBe(
-      "Invalid character(s) detected and removed: -, - "
-    );
+    expect(warnings[0]).toBe("Invalid character(s) detected and removed: - ");
     expect(str).toBe("tataga");
   });
   it("should handle additional chars option", () => {
@@ -51,7 +45,7 @@ describe("filterSequenceString", () => {
     );
     // expect(warnings[0]).toBe(`Replaced "." with "*" 2 times`);
     expect(warnings[0]).toBe(
-      'Invalid character(s) detected and removed: 3, 4, 2, ", ", ", ,, ,, ., ., / '
+      'Invalid character(s) detected and removed: 3, 4, 2, ", ,, ., / '
     );
     expect(str).toBe("bbbxtgalmfwkqespvicyhrnd");
   });

package/src/getComplementSequenceString.js

@@ -1,9 +1,8 @@
 import DNAComplementMap from "./DNAComplementMap";
 import { merge } from "lodash";
 
-// ac.throw([ac.string,ac.bool],arguments);
 export default function getComplementSequenceString(sequence, isRna) {
-  // ac.throw([ac.string],arguments);
+  if (typeof sequence !== "string") return "";
   let complementSeqString = "";
   const complementMap = merge(
     DNAComplementMap,

package/src/getOrfsFromSequence.js

@@ -4,21 +4,13 @@ import getReverseComplementSequenceString from "./getReverseComplementSequenceSt
 /**
  * @private
  * Finds ORFs in a given DNA forward in a given frame.
- * @param  {Int} frame The frame to look in.
- * @param  {String}sequence The dna sequence.
- * @param  {Int} minimumOrfSize The minimum length of ORF to return.
- * @param  {boolean} forward Should we find forward facing orfs or reverse facing orfs
- * @return {Teselagen.bio.orf.ORF[]} The list of ORFs found.
+ * frame - The frame to look in.
+ * sequence - The dna sequence.
+ * minimumOrfSize - The minimum length of ORF to return.
+ * forward - Should we find forward facing orfs or reverse facing orfs
+ * return - The list of ORFs found.
  */
 export default function getOrfsFromSequence(options) {
-  // ac.throw([ac.shape({
-  //     sequence: ac.string,
-  //     minimumOrfSize: ac.posInt,
-  //     forward: ac.bool,
-  //     circular: ac.bool
-  // })], arguments);
-
-  // const frame = options.frame;
   let sequence = options.sequence;
   const minimumOrfSize = options.minimumOrfSize;
   const forward = options.forward;
@@ -38,7 +30,6 @@ export default function getOrfsFromSequence(options) {
   const re = useAdditionalOrfStartCodons
     ? /(?=((?:A[TU]G|G[TU]G|C[TU]G)(?:.{3})*?(?:[TU]AG|[TU]AA|[TU]GA)))/gi
     : /(?=((?:A[TU]G)(?:.{3})*?(?:[TU]AG|[TU]AA|[TU]GA)))/gi;
-  // const str = 'tatgaatgaatgffffffatgfftaaftaafatgfatgfffffsdfatgffatgfffstaafftaafffffffffffffffatgtaaataa\n\natgffftaaf\n\natgffatgftaafftaa\n\natgatgftaafftaa\n\natgatgtaataa\n\ntttttttttttttaatgatgfffffffffftaa';
   let m;
   const orfRanges = [];
   //loop through orf hits!
@@ -103,8 +94,6 @@ export default function getOrfsFromSequence(options) {
     } else {
       orfEnds[orf.end] = index;
       if (!forward) {
-        // if (originalSequenceLength - orf.end - 1 == 3657) {
-        // }
         //this check needs to come after the above assignment of orfEnds
         //flip the start and ends
         const endHolder = orf.end; //temp variable