@teselagen/sequence-utils 0.3.12 → 0.3.14

package/filterSequenceString.d.ts

@@ -1,4 +1,4 @@
-export default function filterSequenceString(sequenceString: any, { additionalValidChars, isOligo, name, isProtein, isRna, isMixedRnaAndDna }?: {
+export default function filterSequenceString(sequenceString?: string, { additionalValidChars, isOligo, name, isProtein, isRna, isMixedRnaAndDna }?: {
     additionalValidChars?: string | undefined;
     isOligo: any;
     name: any;
@@ -22,3 +22,4 @@ export function getReplaceChars({ isOligo, isProtein, isRna, isMixedRnaAndDna }?
 } | {
     t: string;
 };
+export function filterRnaString(s: any, o: any): string | string[];

package/index.d.ts

@@ -20,7 +20,6 @@ export { default as aliasedEnzymesByName } from "./aliasedEnzymesByName";
 export { default as defaultEnzymesByName } from "./defaultEnzymesByName";
 export { default as generateSequenceData } from "./generateSequenceData";
 export { default as generateAnnotations } from "./generateAnnotations";
-export { default as filterSequenceString } from "./filterSequenceString";
 export { default as findNearestRangeOfSequenceOverlapToPosition } from "./findNearestRangeOfSequenceOverlapToPosition";
 export { default as findOrfsInPlasmid } from "./findOrfsInPlasmid";
 export { default as findSequenceMatches } from "./findSequenceMatches";
@@ -82,3 +81,4 @@ import { autoAnnotate } from "./autoAnnotate";
 import { convertApELikeRegexToRegex } from "./autoAnnotate";
 import { convertProteinSeqToDNAIupac } from "./autoAnnotate";
 export { getFeatureToColorMap, getFeatureTypes, genbankFeatureTypes, getMergedFeatureMap, autoAnnotate, convertApELikeRegexToRegex, convertProteinSeqToDNAIupac };
+export { default as filterSequenceString, filterRnaString } from "./filterSequenceString";

package/index.js

@@ -12323,7 +12323,7 @@ const modifiableTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, {
+function filterSequenceString(sequenceString = "", {
   additionalValidChars = "",
   isOligo,
   name,
@@ -12408,6 +12408,7 @@ function getReplaceChars({
   );
 }
 __name(getReplaceChars, "getReplaceChars");
+const filterRnaString = /* @__PURE__ */ __name((s, o) => filterSequenceString(s, __spreadProps(__spreadValues({}, o), { isRna: true }))[0], "filterRnaString");
 function tidyUpAnnotation(_annotation, {
   sequenceData = {},
   convertAnnotationsFromAAIndices,
@@ -13328,11 +13329,12 @@ function adjustAnnotationsToInsert(annotationsToBeAdjusted, insertStart, insertL
 __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
 function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
   const { maintainOriginSplit } = options;
-  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
-  const sequenceDataToInsert = tidyUpSequenceData(
-    _sequenceDataToInsert,
-    options
-  );
+  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
+  const sequenceDataToInsert = tidyUpSequenceData(_sequenceDataToInsert, __spreadValues({
+    topLevelSeqData: existingSequenceData
+  }, options));
   const newSequenceData = lodashExports.cloneDeep(existingSequenceData);
   const insertLength = sequenceDataToInsert.proteinSequence ? sequenceDataToInsert.proteinSequence.length * 3 : sequenceDataToInsert.sequence.length;
   let caretPosition = caretPositionOrRange;
@@ -21354,10 +21356,13 @@ function getAminoAcidStringFromSequenceString(sequenceString) {
   );
   const aaArray = [];
   let aaString = "";
-  aminoAcidsPerBase.forEach((aa) => {
+  aminoAcidsPerBase.forEach((aa, index) => {
     if (!aa.fullCodon) {
       return;
     }
+    if (index === aminoAcidsPerBase.length - 1 && aa.aminoAcid.value === "*") {
+      return;
+    }
     aaArray[aa.aminoAcidIndex] = aa.aminoAcid.value;
   });
   aaString = aaArray.join("");
@@ -21541,7 +21546,9 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
   if (!range)
     return seqData;
   const { exclude = {}, excludePartial = {} } = options;
-  const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+  const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
   annotationTypes.forEach((type) => {
     delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
   });
@@ -21592,9 +21599,13 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
         }
       });
     });
-    return tidyUpSequenceData(toRet, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+    return tidyUpSequenceData(toRet, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
-  return tidyUpSequenceData(seqDataToReturn, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+  return tidyUpSequenceData(seqDataToReturn, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
 function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21641,7 +21652,9 @@ function getComplementSequenceAndAnnotations(pSeqObj, options = {}) {
   const newSeqObj = Object.assign({}, seqObj, {
     sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
   });
-  return tidyUpSequenceData(newSeqObj, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+  return tidyUpSequenceData(newSeqObj, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
 function getCutsiteType(restrictionEnzyme) {
@@ -22736,6 +22749,7 @@ exports.degenerateRnaToAminoAcidMap = degenerateRnaToAminoAcidMap;
 exports.deleteSequenceDataAtRange = deleteSequenceDataAtRange;
 exports.doesEnzymeChopOutsideOfRecognitionSite = doesEnzymeChopOutsideOfRecognitionSite;
 exports.featureColors = featureColors;
+exports.filterRnaString = filterRnaString;
 exports.filterSequenceString = filterSequenceString;
 exports.findNearestRangeOfSequenceOverlapToPosition = findNearestRangeOfSequenceOverlapToPosition;
 exports.findOrfsInPlasmid = findOrfsInPlasmid;

package/index.mjs

@@ -12321,7 +12321,7 @@ const modifiableTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, {
+function filterSequenceString(sequenceString = "", {
   additionalValidChars = "",
   isOligo,
   name,
@@ -12406,6 +12406,7 @@ function getReplaceChars({
   );
 }
 __name(getReplaceChars, "getReplaceChars");
+const filterRnaString = /* @__PURE__ */ __name((s, o) => filterSequenceString(s, __spreadProps(__spreadValues({}, o), { isRna: true }))[0], "filterRnaString");
 function tidyUpAnnotation(_annotation, {
   sequenceData = {},
   convertAnnotationsFromAAIndices,
@@ -13326,11 +13327,12 @@ function adjustAnnotationsToInsert(annotationsToBeAdjusted, insertStart, insertL
 __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
 function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
   const { maintainOriginSplit } = options;
-  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
-  const sequenceDataToInsert = tidyUpSequenceData(
-    _sequenceDataToInsert,
-    options
-  );
+  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
+  const sequenceDataToInsert = tidyUpSequenceData(_sequenceDataToInsert, __spreadValues({
+    topLevelSeqData: existingSequenceData
+  }, options));
   const newSequenceData = lodashExports.cloneDeep(existingSequenceData);
   const insertLength = sequenceDataToInsert.proteinSequence ? sequenceDataToInsert.proteinSequence.length * 3 : sequenceDataToInsert.sequence.length;
   let caretPosition = caretPositionOrRange;
@@ -21352,10 +21354,13 @@ function getAminoAcidStringFromSequenceString(sequenceString) {
   );
   const aaArray = [];
   let aaString = "";
-  aminoAcidsPerBase.forEach((aa) => {
+  aminoAcidsPerBase.forEach((aa, index) => {
     if (!aa.fullCodon) {
       return;
     }
+    if (index === aminoAcidsPerBase.length - 1 && aa.aminoAcid.value === "*") {
+      return;
+    }
     aaArray[aa.aminoAcidIndex] = aa.aminoAcid.value;
   });
   aaString = aaArray.join("");
@@ -21539,7 +21544,9 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
   if (!range)
     return seqData;
   const { exclude = {}, excludePartial = {} } = options;
-  const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+  const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
   annotationTypes.forEach((type) => {
     delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
   });
@@ -21590,9 +21597,13 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
         }
       });
     });
-    return tidyUpSequenceData(toRet, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+    return tidyUpSequenceData(toRet, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
-  return tidyUpSequenceData(seqDataToReturn, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+  return tidyUpSequenceData(seqDataToReturn, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
 function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21639,7 +21650,9 @@ function getComplementSequenceAndAnnotations(pSeqObj, options = {}) {
   const newSeqObj = Object.assign({}, seqObj, {
     sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
   });
-  return tidyUpSequenceData(newSeqObj, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+  return tidyUpSequenceData(newSeqObj, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
 function getCutsiteType(restrictionEnzyme) {
@@ -22735,6 +22748,7 @@ export {
   deleteSequenceDataAtRange,
   doesEnzymeChopOutsideOfRecognitionSite,
   featureColors,
+  filterRnaString,
   filterSequenceString,
   findNearestRangeOfSequenceOverlapToPosition,
   findOrfsInPlasmid,

package/index.umd.js

@@ -12325,7 +12325,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     "primers",
     "guides"
   ];
-  function filterSequenceString(sequenceString, {
+  function filterSequenceString(sequenceString = "", {
     additionalValidChars = "",
     isOligo,
     name,
@@ -12410,6 +12410,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     );
   }
   __name(getReplaceChars, "getReplaceChars");
+  const filterRnaString = /* @__PURE__ */ __name((s, o) => filterSequenceString(s, __spreadProps(__spreadValues({}, o), { isRna: true }))[0], "filterRnaString");
   function tidyUpAnnotation(_annotation, {
     sequenceData = {},
     convertAnnotationsFromAAIndices,
@@ -13330,11 +13331,12 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
   function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
     const { maintainOriginSplit } = options;
-    let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
-    const sequenceDataToInsert = tidyUpSequenceData(
-      _sequenceDataToInsert,
-      options
-    );
+    let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
+    const sequenceDataToInsert = tidyUpSequenceData(_sequenceDataToInsert, __spreadValues({
+      topLevelSeqData: existingSequenceData
+    }, options));
     const newSequenceData = lodashExports.cloneDeep(existingSequenceData);
     const insertLength = sequenceDataToInsert.proteinSequence ? sequenceDataToInsert.proteinSequence.length * 3 : sequenceDataToInsert.sequence.length;
     let caretPosition = caretPositionOrRange;
@@ -21356,10 +21358,13 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     );
     const aaArray = [];
     let aaString = "";
-    aminoAcidsPerBase.forEach((aa) => {
+    aminoAcidsPerBase.forEach((aa, index) => {
       if (!aa.fullCodon) {
         return;
       }
+      if (index === aminoAcidsPerBase.length - 1 && aa.aminoAcid.value === "*") {
+        return;
+      }
       aaArray[aa.aminoAcidIndex] = aa.aminoAcid.value;
     });
     aaString = aaArray.join("");
@@ -21543,7 +21548,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     if (!range)
       return seqData;
     const { exclude = {}, excludePartial = {} } = options;
-    const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+    const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
     annotationTypes.forEach((type) => {
       delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
     });
@@ -21594,9 +21601,13 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
           }
         });
       });
-      return tidyUpSequenceData(toRet, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+      return tidyUpSequenceData(toRet, __spreadValues({
+        doNotRemoveInvalidChars: true
+      }, options));
     }
-    return tidyUpSequenceData(seqDataToReturn, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+    return tidyUpSequenceData(seqDataToReturn, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
   __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
   function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21643,7 +21654,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     const newSeqObj = Object.assign({}, seqObj, {
       sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
     });
-    return tidyUpSequenceData(newSeqObj, __spreadValues({ doNotRemoveInvalidChars: true }, options));
+    return tidyUpSequenceData(newSeqObj, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
   __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
   function getCutsiteType(restrictionEnzyme) {
@@ -22738,6 +22751,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   exports2.deleteSequenceDataAtRange = deleteSequenceDataAtRange;
   exports2.doesEnzymeChopOutsideOfRecognitionSite = doesEnzymeChopOutsideOfRecognitionSite;
   exports2.featureColors = featureColors;
+  exports2.filterRnaString = filterRnaString;
   exports2.filterSequenceString = filterSequenceString;
   exports2.findNearestRangeOfSequenceOverlapToPosition = findNearestRangeOfSequenceOverlapToPosition;
   exports2.findOrfsInPlasmid = findOrfsInPlasmid;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.12",
+  "version": "0.3.14",
   "dependencies": {
     "@teselagen/range-utils": "0.3.7",
     "bson-objectid": "^2.0.4",

package/src/filterSequenceString.js

@@ -5,7 +5,7 @@ import {
 } from "./bioData";
 
 export default function filterSequenceString(
-  sequenceString,
+  sequenceString = "",
   {
     additionalValidChars = "",
     isOligo,
@@ -111,3 +111,6 @@ export function getReplaceChars({
     : //just plain old dna
       {};
 }
+
+export const filterRnaString = (s, o) =>
+  filterSequenceString(s, { ...o, isRna: true })[0];

package/src/getAminoAcidStringFromSequenceString.js

@@ -7,10 +7,14 @@ export default function getAminoAcidStringFromSequenceString(sequenceString) {
   );
   const aaArray = [];
   let aaString = "";
-  aminoAcidsPerBase.forEach(aa => {
+  aminoAcidsPerBase.forEach((aa, index) => {
     if (!aa.fullCodon) {
       return;
     }
+    // Check if the current amino acid is the last in the sequence and is a stop codon
+    if (index === aminoAcidsPerBase.length - 1 && aa.aminoAcid.value === '*') {
+      return;
+    }
     aaArray[aa.aminoAcidIndex] = aa.aminoAcid.value;
   });
   aaString = aaArray.join("");

package/src/getAminoAcidStringFromSequenceString.test.js

@@ -14,5 +14,6 @@ describe("getAminoAcidStringFromSequenceString", () => {
     assert.equal("MM", getAminoAcidStringFromSequenceString("atgatg"));
     assert.equal("M--", getAminoAcidStringFromSequenceString("atg------"));
     assert.equal("", getAminoAcidStringFromSequenceString("at"));
+    assert.equal("MTNYNQKNEN", getAminoAcidStringFromSequenceString("atgactaattataatcaaaaaaatgaaaattaa"));
   });
 });

package/src/getComplementSequenceAndAnnotations.js

@@ -15,5 +15,8 @@ export default function getComplementSequenceAndAnnotations(
   const newSeqObj = Object.assign({}, seqObj, {
     sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
   });
-  return tidyUpSequenceData(newSeqObj, {doNotRemoveInvalidChars: true,...options});
+  return tidyUpSequenceData(newSeqObj, {
+    doNotRemoveInvalidChars: true,
+    ...options
+  });
 }

package/src/getSequenceDataBetweenRange.js

@@ -16,7 +16,10 @@ export default function getSequenceDataBetweenRange(
 ) {
   if (!range) return seqData;
   const { exclude = {}, excludePartial = {} } = options;
-  const seqDataToUse = tidyUpSequenceData(seqData, {doNotRemoveInvalidChars: true,...options});
+  const seqDataToUse = tidyUpSequenceData(seqData, {
+    doNotRemoveInvalidChars: true,
+    ...options
+  });
   annotationTypes.forEach(type => {
     delete seqDataToUse[`filtered${startCase(type)}`];
   });
@@ -78,10 +81,16 @@ export default function getSequenceDataBetweenRange(
         }
       });
     });
-    return tidyUpSequenceData(toRet, {doNotRemoveInvalidChars: true,...options});
+    return tidyUpSequenceData(toRet, {
+      doNotRemoveInvalidChars: true,
+      ...options
+    });
   }
 
-  return tidyUpSequenceData(seqDataToReturn, {doNotRemoveInvalidChars: true,...options});
+  return tidyUpSequenceData(seqDataToReturn, {
+    doNotRemoveInvalidChars: true,
+    ...options
+  });
 }
 
 function getAnnotationsBetweenRange(

package/src/index.js

@@ -51,7 +51,10 @@ export { default as aliasedEnzymesByName } from "./aliasedEnzymesByName";
 export { default as defaultEnzymesByName } from "./defaultEnzymesByName";
 export { default as generateSequenceData } from "./generateSequenceData";
 export { default as generateAnnotations } from "./generateAnnotations";
-export { default as filterSequenceString } from "./filterSequenceString";
+export {
+  default as filterSequenceString,
+  filterRnaString
+} from "./filterSequenceString";
 export { default as findNearestRangeOfSequenceOverlapToPosition } from "./findNearestRangeOfSequenceOverlapToPosition";
 export { default as findOrfsInPlasmid } from "./findOrfsInPlasmid";
 export { default as findSequenceMatches } from "./findSequenceMatches";

package/src/insertSequenceDataAtPositionOrRange.js

@@ -18,11 +18,14 @@ export default function insertSequenceDataAtPositionOrRange(
   //when inserting new seq, n bps of the new seq should go in before the origin and the rest should be
   //inserted at the sequence start
   const { maintainOriginSplit } = options;
-  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, {doNotRemoveInvalidChars: true,...options});
-  const sequenceDataToInsert = tidyUpSequenceData(
-    _sequenceDataToInsert,
-    options
-  );
+  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, {
+    doNotRemoveInvalidChars: true,
+    ...options
+  });
+  const sequenceDataToInsert = tidyUpSequenceData(_sequenceDataToInsert, {
+    topLevelSeqData: existingSequenceData,
+    ...options
+  });
   const newSequenceData = cloneDeep(existingSequenceData);
   const insertLength = sequenceDataToInsert.proteinSequence
     ? sequenceDataToInsert.proteinSequence.length * 3