@teselagen/sequence-utils 0.3.24 → 0.3.26

package/insertSequenceDataAtPosition.d.ts

@@ -1,2 +1,2 @@
+import { default as insertSequenceDataAtPositionOrRange } from './insertSequenceDataAtPositionOrRange';
 export default insertSequenceDataAtPositionOrRange;
-import insertSequenceDataAtPositionOrRange from "./insertSequenceDataAtPositionOrRange";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.24",
+  "version": "0.3.26",
   "dependencies": {
     "@teselagen/range-utils": "0.3.7",
     "bson-objectid": "^2.0.4",

package/src/addGapsToSeqReads.js

@@ -1,6 +1,6 @@
 import insertGapsIntoRefSeq from "./insertGapsIntoRefSeq.js";
 
-import { cloneDeep } from "lodash";
+import { cloneDeep } from "lodash-es";
 
 // bam.seq: NTGTAAGTCGTGAAAAAANCNNNCATATTNCGGAGGTAAAAATGAAAA...
 // bam.pos: 43

package/src/adjustAnnotationsToInsert.js

@@ -1,5 +1,5 @@
 import { adjustRangeToInsert } from "@teselagen/range-utils";
-import { map } from "lodash";
+import { map } from "lodash-es";
 
 export default function adjustAnnotationsToInsert(
   annotationsToBeAdjusted,

package/src/autoAnnotate.js

@@ -1,5 +1,5 @@
 /* Copyright (C) 2018 TeselaGen Biotechnology, Inc. */
-import { forEach, omitBy } from "lodash";
+import { forEach, omitBy } from "lodash-es";
 import { ambiguous_dna_values } from "./bioData";
 import aminoAcidToDegenerateDnaMap from "./aminoAcidToDegenerateDnaMap";
 import {

package/src/calculateNebTm.js

@@ -9,8 +9,7 @@ import calculatePercentGc from "./calculatePercentGC";
 // primer concentration & monovalent cation concentration in M
 export default function calculateNebTm(
   sequence,
-  primerConc,
-  { monovalentCationConc } = {}
+  { monovalentCationConc = 0.05, primerConc = 0.0000005 } = {}
 ) {
   try {
     const checkForDegenerateBases = /[^atgc]/i.test(sequence);

package/src/calculateNebTm.test.js

@@ -1,31 +1,40 @@
 import assert from "assert";
-import calculateTm from "./calculateNebTm";
+import calculateNebTm from "./calculateNebTm";
+// import calculateTm from "./calculateTm";
 
 describe("calculate Tm based on SantaLucia 1998 & Owczarzy 2004", () => {
   it("should return the melting temperature of a given sequence, if no degenerate bases are present", () => {
     const options = {
       // 50 mM KCl in Q5 protocol
-      monovalentCationConc: 0.05
+      monovalentCationConc: 0.05,
+      primerConc: 0.0000005
     };
+    // console.log(`calculateNebTm("AGCGGATAACAATTTCACACAGGA", options),:`,calculateNebTm("AGCGGATAACAATTTCACACAGGA", options),)
+    // console.log(`calculateTm("AGCGGATAACAATTTCACACAGGA", options),:`,calculateTm("AGCGGATAACAATTTCACACAGGA", options),)
+    // console.log(`calculateTm("AGCGGATAnbACdAATTTCACACANNGGA", options),:`,calculateTm("AGCGGATAACAATTTCACACAGGA", options),)
     // primer concentration in Q5 protocol is 500 nM
     assert.equal(
-      calculateTm("AGCGGATAACAATTTCACACAGGA", 0.0000005, options),
+      calculateNebTm("AGCGGATAACAATTTCACACAGGA", options),
       65.8994505801345
     );
     assert.equal(
-      calculateTm("AGCGGATAACAATTTCAC", 0.0000005, options),
+      calculateNebTm("AGCGGATAACAATTTCAC", options),
       56.11037835109477
     );
     assert.equal(
-      calculateTm("AGCGGATAACAATTTcac", 0.0000005, options),
+      calculateNebTm("AGCGGATAACAATTTcac", options),
       56.11037835109477
     );
     assert.equal(
-      calculateTm("AGCGGNNN", 0.0000005, options),
+      calculateNebTm("ataataccgcgccacatagc", options),
+      65.03019485849268
+    );
+    assert.equal(
+      calculateNebTm("AGCGGNNN", options),
       "Error calculating Tm for sequence AGCGGNNN: Error: Degenerate bases prohibited in Tm calculation of sequence AGCGGNNN"
     );
     assert.equal(
-      calculateTm("AGCGGnnn", 0.0000005, options),
+      calculateNebTm("AGCGGnnn", options),
       "Error calculating Tm for sequence AGCGGnnn: Error: Degenerate bases prohibited in Tm calculation of sequence AGCGGnnn"
     );
   });

package/src/calculateTm.js

@@ -11,8 +11,8 @@ const calcTmMethods = {
 
   A: -10.8, // Helix initiation for deltaS
   R: 1.987, // Gas constant (cal/(K*mol)).
-  C: 0.5e-6, // Oligo concentration. 0.5uM is typical for PCR.
-  Na: 50e-3, // Monovalent salt concentration. 50mM is typical for PCR.
+  primerConc: 0.0000005, // Oligo concentration. 0.5uM is typical for PCR.
+  monovalentCationConc: 0.05, // Monovalent salt concentration. 50mM is typical for PCR.
 
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
@@ -20,11 +20,17 @@ const calcTmMethods = {
    * 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.
+   * monovalentCationConc - THe monovalent salt concentration. Defaults to 50e-3M.
    * return - Temperature for the given sequence, in Celsius.
    */
-  calculateTemperature: function (sequence, type, A, R, C, Na) {
+  calculateTemperature: function (
+    _sequence,
+    { type, A, R, primerConc, monovalentCationConc } = {}
+  ) {
+    const sequence = _sequence.toLowerCase();
     if (typeof type === "undefined") {
+      // type = this.TABLE_SUGIMOTO  ;
+      // type = this.TABLE_UNIFIED;
       type = this.TABLE_BRESLAUER;
     } else if (
       type != this.TABLE_BRESLAUER &&
@@ -40,11 +46,11 @@ const calcTmMethods = {
     if (!R) {
       R = this.R;
     }
-    if (!C) {
-      C = this.C;
+    if (!primerConc) {
+      primerConc = this.primerConc;
     }
-    if (!Na) {
-      Na = this.Na;
+    if (!monovalentCationConc) {
+      monovalentCationConc = this.monovalentCationConc;
     }
 
     const sequenceLength = sequence.length;
@@ -56,7 +62,7 @@ const calcTmMethods = {
     const deltaHTable = this.getDeltaHTable(type);
     const deltaSTable = this.getDeltaSTable(type);
 
-    const neighbors = []; // List goes in order: aa, at, ac, ag, tt, ta, tc, tg, cc, ca, ct, cg, gg, gt, gc
+    const neighbors = []; // List goes in order: aa, at, ac, ag, tt, ta, tc, tg, cc, ca, ct, cg, gg, ga, gt, gc
 
     neighbors.push(this.calculateReps(sequence, "aa"));
     neighbors.push(this.calculateNumberOfOccurrences(sequence, "at"));
@@ -87,16 +93,12 @@ const calcTmMethods = {
     }
 
     const temperature =
-      (-1000.0 * sumDeltaH) / (A + -sumDeltaS + R * Math.log(C / 4.0)) -
+      (-1000.0 * sumDeltaH) /
+        (A + -sumDeltaS + R * Math.log(primerConc / 4.0)) -
       273.15 +
-      16.6 * Math.LOG10E * Math.log(Na);
+      16.6 * Math.LOG10E * Math.log(monovalentCationConc);
 
-    // If temperature is negative then return 0.
-    if (temperature < 0) {
-      return 0;
-    }
-
-    return temperature.toFixed(2);
+    return temperature;
   },
 
   /**
@@ -125,6 +127,41 @@ const calcTmMethods = {
       return null;
     }
   },
+  // "AA/TT": -7.9, 7.9
+  // "AT/TA": -7.2, 7.2
+  // "AC/TG": -8.4, 8.4
+  // "AG/TC": -7.8, 7.8
+  // "TT/AA": -7.9, 7.9
+  // "TA/AT": -7.2, 7.2
+  // "TG/AC": -8.5, 8.2
+  // "TC/AG": -8.2, 8.5
+  // "CC/GG": -8.0, 8.0
+  // "CA/GT": -8.5, 8.5
+  // "CT/GA": -7.8, 7.8
+  // "CG/GC": -10.6, 10.6
+  // "GG/CC": -8.0, 8.0
+  // "GA/CT": -8.2, 8.2,
+  // "GT/CA": -8.4, 8.4
+  // "GC/CG": -9.8, 9.8
+
+  // aa, at, ac, ag, tt, ta, tc, tg, cc, ca, ct, cg, gg, ga, gt, gc
+
+  // "AA/TT": -22.2,22.2,
+  // "AT/TA": -20.4,20.4,
+  // "AC/TG": -22.4,22.4,
+  // "AG/TC": -21.0,21.0,
+  // "TT/AA": -22.2,22.2,
+  // "TA/AT": -21.3,21.3,
+  // "TC/AG": -22.2,22.2,
+  // "TG/AC": -22.7,22.7,
+  // "CC/GG": -19.9,19.9,
+  // "CA/GT": -22.7,22.7,
+  // "CT/GA": -21.0,21.0,
+  // "CG/GC": -27.2,27.2,
+  // "GG/CC": -19.9,19.9,
+  // "GT/CA": -22.4,22.2,
+  // "GA/CT": -22.2,22.4,
+  // "GC/CG": -24.4,24.4
 
   /**
    * @private

package/src/calculateTm.test.js

@@ -2,6 +2,12 @@ import calculateTm from "./calculateTm";
 import assert from "assert";
 describe("calculateTm", () => {
   it("should calculate the correct tm", () => {
-    assert.equal(calculateTm("atagagaggga"), 26.21);
+    assert.equal(calculateTm("atagagaggga"), 26.211404758492115);
+    assert.equal(calculateTm("AGCGGATAACAATTTCACACAGGA"), 67.27154960706082);
+    assert.equal(calculateTm("AGCGGATAACAATTTCAC"), 54.91103113095034);
+    assert.equal(calculateTm("AGCGGATAACAATTTcac"), 54.91103113095034);
+    assert.equal(calculateTm("ataataccgcgccacatagc"), 63.51394755261396);
+    assert.equal(calculateTm("AGCGGNNN"), -5.0392194500109255);
+    assert.equal(calculateTm("AGCGGnnn"), -5.0392194500109255);
   });
 });

package/src/computeDigestFragments.js

@@ -1,5 +1,5 @@
 import shortid from "shortid";
-import { flatMap, cloneDeep } from "lodash";
+import { flatMap, cloneDeep } from "lodash-es";
 import {
   normalizePositionByRangeLength,
   getRangeLength

package/src/cutSequenceByRestrictionEnzyme.js

@@ -1,4 +1,4 @@
-import { assign } from "lodash";
+import { assign } from "lodash-es";
 import shortid from "shortid";
 import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 

package/src/degenerateDnaToAminoAcidMap.js

@@ -1,4 +1,4 @@
-import { invert } from "lodash";
+import { invert } from "lodash-es";
 import aminoAcidToDegenerateDnaMap from "./aminoAcidToDegenerateDnaMap";
 
 const degenerateDnaToAminoAcidMap = invert(aminoAcidToDegenerateDnaMap);

package/src/degenerateRnaToAminoAcidMap.js

@@ -1,4 +1,4 @@
-import { invert } from "lodash";
+import { invert } from "lodash-es";
 import aminoAcidToDegenerateRnaMap from "./aminoAcidToDegenerateRnaMap";
 
 const degenerateRnaToAminoAcidMap = invert(aminoAcidToDegenerateRnaMap);

package/src/deleteSequenceDataAtRange.test.js

@@ -3,7 +3,7 @@
 import chai from "chai";
 
 import { getRangeLength } from "@teselagen/range-utils";
-import { cloneDeep } from "lodash";
+import { cloneDeep } from "lodash-es";
 import chaiSubset from "chai-subset";
 
 import deleteSequenceDataAtRange from "./deleteSequenceDataAtRange";

package/src/diffUtils.js

@@ -1,4 +1,4 @@
-import { cloneDeep, forEach } from "lodash";
+import { cloneDeep, forEach } from "lodash-es";
 import { diff, patch, reverse } from "jsondiffpatch/dist/jsondiffpatch.umd";
 
 import tidyUpSequenceData from "./tidyUpSequenceData";

package/src/diffUtils.test.js

@@ -1,6 +1,6 @@
 import chai from "chai";
 import assert from "assert";
-import { map } from "lodash";
+import { map } from "lodash-es";
 import tidyUpSequenceData from "./tidyUpSequenceData";
 import { getDiffFromSeqs, patchSeqWithDiff, reverseSeqDiff } from "./diffUtils";
 import chaiSubset from "chai-subset";

package/src/featureTypesAndColors.js

@@ -1,4 +1,4 @@
-import { get, keyBy, filter } from "lodash";
+import { get, keyBy, filter } from "lodash-es";
 
 const genbankFeatureTypes = [
   { name: "-10_signal", color: "#4ECDC4" },

package/src/filterSequenceString.js

@@ -1,4 +1,4 @@
-import { debounce, uniq } from "lodash";
+import { debounce, uniq } from "lodash-es";
 import {
   ambiguous_dna_letters,
   ambiguous_rna_letters,

package/src/findSequenceMatches.js

@@ -2,7 +2,7 @@ import {
   modulateRangeBySequenceLength,
   flipContainedRange
 } from "@teselagen/range-utils";
-import { reduce, uniqBy } from "lodash";
+import { reduce, uniqBy } from "lodash-es";
 import escapeStringRegexp from "escape-string-regexp";
 import getAminoAcidStringFromSequenceString from "./getAminoAcidStringFromSequenceString";
 import { ambiguous_dna_values, extended_protein_values } from "./bioData";

package/src/generateSequenceData.test.js

@@ -1,7 +1,7 @@
 import generateSequenceData from "./generateSequenceData";
 import chai from "chai";
 import chaiSubset from "chai-subset";
-import { map } from "lodash";
+import { map } from "lodash-es";
 
 chai.should();
 chai.use(chaiSubset);