@teselagen/sequence-utils 0.3.11 → 0.3.13

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,
@@ -12675,11 +12676,13 @@ __name(tidyUpSequenceData, "tidyUpSequenceData");
 const getDiffFromSeqs = /* @__PURE__ */ __name((oldData, newData, { ignoreKeys = [] } = {}) => {
   oldData = tidyUpSequenceData(oldData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   newData = tidyUpSequenceData(newData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   [oldData, newData].forEach((d) => {
     [
@@ -12711,7 +12714,10 @@ const patchSeqWithDiff = /* @__PURE__ */ __name((oldData, diff, { ignoreKeys = [
     delete diff[k];
   });
   return jsondiffpatch_umdExports.patch(
-    tidyUpSequenceData(lodashExports.cloneDeep(oldData), { annotationsAsObjects: true }),
+    tidyUpSequenceData(lodashExports.cloneDeep(oldData), {
+      annotationsAsObjects: true,
+      doNotRemoveInvalidChars: true
+    }),
     diff
   );
 }, "patchSeqWithDiff");
@@ -13284,7 +13290,9 @@ function arrayRotate(arr, count) {
 }
 __name(arrayRotate, "arrayRotate");
 function rotateSequenceDataToPosition(sequenceData, caretPosition, options) {
-  const newSequenceData = tidyUpSequenceData(sequenceData, options);
+  const newSequenceData = tidyUpSequenceData(sequenceData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
   newSequenceData.sequence = rotateBpsToPosition(
     newSequenceData.sequence,
     caretPosition
@@ -13321,11 +13329,12 @@ function adjustAnnotationsToInsert(annotationsToBeAdjusted, insertStart, insertL
 __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
 function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
   const { maintainOriginSplit } = options;
-  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, 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;
@@ -13339,6 +13348,7 @@ function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSeq
         return acc[type] = [];
       }, {})), {
         sequence: "",
+        doNotRemoveInvalidChars: true,
         proteinSequence: "",
         chromatogramData: void 0
       }),
@@ -21533,7 +21543,9 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
   if (!range)
     return seqData;
   const { exclude = {}, excludePartial = {} } = options;
-  const seqDataToUse = tidyUpSequenceData(seqData, options);
+  const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
   annotationTypes.forEach((type) => {
     delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
   });
@@ -21584,9 +21596,13 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
         }
       });
     });
-    return tidyUpSequenceData(toRet, options);
+    return tidyUpSequenceData(toRet, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
-  return tidyUpSequenceData(seqDataToReturn, options);
+  return tidyUpSequenceData(seqDataToReturn, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
 function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21633,7 +21649,9 @@ function getComplementSequenceAndAnnotations(pSeqObj, options = {}) {
   const newSeqObj = Object.assign({}, seqObj, {
     sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
   });
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
 function getCutsiteType(restrictionEnzyme) {
@@ -21839,7 +21857,7 @@ __name(getReverseComplementAnnotation, "getReverseComplementAnnotation");
 function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
   const seqObj = tidyUpSequenceData(
     getSequenceDataBetweenRange(pSeqObj, options.range),
-    options
+    __spreadValues({ doNotRemoveInvalidChars: true }, options)
   );
   const newSeqObj = Object.assign(
     {},
@@ -21859,7 +21877,9 @@ function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
       return acc;
     }, {})
   );
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getReverseComplementSequenceAndAnnoations, "getReverseComplementSequenceAndAnnoations");
 function getReverseSequenceString(sequence) {
@@ -22726,6 +22746,7 @@ 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,
@@ -12673,11 +12674,13 @@ __name(tidyUpSequenceData, "tidyUpSequenceData");
 const getDiffFromSeqs = /* @__PURE__ */ __name((oldData, newData, { ignoreKeys = [] } = {}) => {
   oldData = tidyUpSequenceData(oldData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   newData = tidyUpSequenceData(newData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   [oldData, newData].forEach((d) => {
     [
@@ -12709,7 +12712,10 @@ const patchSeqWithDiff = /* @__PURE__ */ __name((oldData, diff, { ignoreKeys = [
     delete diff[k];
   });
   return jsondiffpatch_umdExports.patch(
-    tidyUpSequenceData(lodashExports.cloneDeep(oldData), { annotationsAsObjects: true }),
+    tidyUpSequenceData(lodashExports.cloneDeep(oldData), {
+      annotationsAsObjects: true,
+      doNotRemoveInvalidChars: true
+    }),
     diff
   );
 }, "patchSeqWithDiff");
@@ -13282,7 +13288,9 @@ function arrayRotate(arr, count) {
 }
 __name(arrayRotate, "arrayRotate");
 function rotateSequenceDataToPosition(sequenceData, caretPosition, options) {
-  const newSequenceData = tidyUpSequenceData(sequenceData, options);
+  const newSequenceData = tidyUpSequenceData(sequenceData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
   newSequenceData.sequence = rotateBpsToPosition(
     newSequenceData.sequence,
     caretPosition
@@ -13319,11 +13327,12 @@ function adjustAnnotationsToInsert(annotationsToBeAdjusted, insertStart, insertL
 __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
 function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
   const { maintainOriginSplit } = options;
-  let existingSequenceData = tidyUpSequenceData(_existingSequenceData, 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;
@@ -13337,6 +13346,7 @@ function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSeq
         return acc[type] = [];
       }, {})), {
         sequence: "",
+        doNotRemoveInvalidChars: true,
         proteinSequence: "",
         chromatogramData: void 0
       }),
@@ -21531,7 +21541,9 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
   if (!range)
     return seqData;
   const { exclude = {}, excludePartial = {} } = options;
-  const seqDataToUse = tidyUpSequenceData(seqData, options);
+  const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
   annotationTypes.forEach((type) => {
     delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
   });
@@ -21582,9 +21594,13 @@ function getSequenceDataBetweenRange(seqData, range, options = {}) {
         }
       });
     });
-    return tidyUpSequenceData(toRet, options);
+    return tidyUpSequenceData(toRet, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
-  return tidyUpSequenceData(seqDataToReturn, options);
+  return tidyUpSequenceData(seqDataToReturn, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
 function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21631,7 +21647,9 @@ function getComplementSequenceAndAnnotations(pSeqObj, options = {}) {
   const newSeqObj = Object.assign({}, seqObj, {
     sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
   });
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
 function getCutsiteType(restrictionEnzyme) {
@@ -21837,7 +21855,7 @@ __name(getReverseComplementAnnotation, "getReverseComplementAnnotation");
 function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
   const seqObj = tidyUpSequenceData(
     getSequenceDataBetweenRange(pSeqObj, options.range),
-    options
+    __spreadValues({ doNotRemoveInvalidChars: true }, options)
   );
   const newSeqObj = Object.assign(
     {},
@@ -21857,7 +21875,9 @@ function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
       return acc;
     }, {})
   );
-  return tidyUpSequenceData(newSeqObj, options);
+  return tidyUpSequenceData(newSeqObj, __spreadValues({
+    doNotRemoveInvalidChars: true
+  }, options));
 }
 __name(getReverseComplementSequenceAndAnnoations, "getReverseComplementSequenceAndAnnoations");
 function getReverseSequenceString(sequence) {
@@ -22725,6 +22745,7 @@ 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,
@@ -12677,11 +12678,13 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   const getDiffFromSeqs = /* @__PURE__ */ __name((oldData, newData, { ignoreKeys = [] } = {}) => {
     oldData = tidyUpSequenceData(oldData, {
       annotationsAsObjects: true,
-      noTranslationData: true
+      noTranslationData: true,
+      doNotRemoveInvalidChars: true
     });
     newData = tidyUpSequenceData(newData, {
       annotationsAsObjects: true,
-      noTranslationData: true
+      noTranslationData: true,
+      doNotRemoveInvalidChars: true
     });
     [oldData, newData].forEach((d) => {
       [
@@ -12713,7 +12716,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       delete diff[k];
     });
     return jsondiffpatch_umdExports.patch(
-      tidyUpSequenceData(lodashExports.cloneDeep(oldData), { annotationsAsObjects: true }),
+      tidyUpSequenceData(lodashExports.cloneDeep(oldData), {
+        annotationsAsObjects: true,
+        doNotRemoveInvalidChars: true
+      }),
       diff
     );
   }, "patchSeqWithDiff");
@@ -13286,7 +13292,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(arrayRotate, "arrayRotate");
   function rotateSequenceDataToPosition(sequenceData, caretPosition, options) {
-    const newSequenceData = tidyUpSequenceData(sequenceData, options);
+    const newSequenceData = tidyUpSequenceData(sequenceData, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
     newSequenceData.sequence = rotateBpsToPosition(
       newSequenceData.sequence,
       caretPosition
@@ -13323,11 +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, 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;
@@ -13341,6 +13350,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
           return acc[type] = [];
         }, {})), {
           sequence: "",
+          doNotRemoveInvalidChars: true,
           proteinSequence: "",
           chromatogramData: void 0
         }),
@@ -21535,7 +21545,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     if (!range)
       return seqData;
     const { exclude = {}, excludePartial = {} } = options;
-    const seqDataToUse = tidyUpSequenceData(seqData, options);
+    const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
     annotationTypes.forEach((type) => {
       delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
     });
@@ -21586,9 +21598,13 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
           }
         });
       });
-      return tidyUpSequenceData(toRet, options);
+      return tidyUpSequenceData(toRet, __spreadValues({
+        doNotRemoveInvalidChars: true
+      }, options));
     }
-    return tidyUpSequenceData(seqDataToReturn, options);
+    return tidyUpSequenceData(seqDataToReturn, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
   __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
   function getAnnotationsBetweenRange(annotationsToBeAdjusted, range, maxLength, shouldExcludePartial) {
@@ -21635,7 +21651,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     const newSeqObj = Object.assign({}, seqObj, {
       sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
     });
-    return tidyUpSequenceData(newSeqObj, options);
+    return tidyUpSequenceData(newSeqObj, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
   __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
   function getCutsiteType(restrictionEnzyme) {
@@ -21841,7 +21859,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
     const seqObj = tidyUpSequenceData(
       getSequenceDataBetweenRange(pSeqObj, options.range),
-      options
+      __spreadValues({ doNotRemoveInvalidChars: true }, options)
     );
     const newSeqObj = Object.assign(
       {},
@@ -21861,7 +21879,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
         return acc;
       }, {})
     );
-    return tidyUpSequenceData(newSeqObj, options);
+    return tidyUpSequenceData(newSeqObj, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
   __name(getReverseComplementSequenceAndAnnoations, "getReverseComplementSequenceAndAnnoations");
   function getReverseSequenceString(sequence) {
@@ -22728,6 +22748,7 @@ 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": "0.3.11",
+  "version": "0.3.13",
   "dependencies": {
     "@teselagen/range-utils": "0.3.7",
     "bson-objectid": "^2.0.4",

package/src/diffUtils.js

@@ -6,11 +6,13 @@ import tidyUpSequenceData from "./tidyUpSequenceData";
 const getDiffFromSeqs = (oldData, newData, { ignoreKeys = [] } = {}) => {
   oldData = tidyUpSequenceData(oldData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
   newData = tidyUpSequenceData(newData, {
     annotationsAsObjects: true,
-    noTranslationData: true
+    noTranslationData: true,
+    doNotRemoveInvalidChars: true
   });
 
   [oldData, newData].forEach(d => {
@@ -47,7 +49,10 @@ const patchSeqWithDiff = (oldData, diff, { ignoreKeys = [] } = {}) => {
     delete diff[k];
   });
   return patch(
-    tidyUpSequenceData(cloneDeep(oldData), { annotationsAsObjects: true }),
+    tidyUpSequenceData(cloneDeep(oldData), {
+      annotationsAsObjects: true,
+      doNotRemoveInvalidChars: true
+    }),
     diff
   );
 };

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/getComplementSequenceAndAnnotations.js

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

package/src/getReverseComplementSequenceAndAnnotations.js

@@ -13,7 +13,7 @@ export default function getReverseComplementSequenceAndAnnoations(
 ) {
   const seqObj = tidyUpSequenceData(
     getSequenceDataBetweenRange(pSeqObj, options.range),
-    options
+    { doNotRemoveInvalidChars: true, ...options }
   );
   const newSeqObj = Object.assign(
     {},
@@ -33,5 +33,8 @@ export default function getReverseComplementSequenceAndAnnoations(
       return acc;
     }, {})
   );
-  return tidyUpSequenceData(newSeqObj, 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, 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, options);
+    return tidyUpSequenceData(toRet, {
+      doNotRemoveInvalidChars: true,
+      ...options
+    });
   }
 
-  return tidyUpSequenceData(seqDataToReturn, 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, 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
@@ -48,6 +51,7 @@ export default function insertSequenceDataAtPositionOrRange(
           return (acc[type] = []);
         }, {}),
         sequence: "",
+        doNotRemoveInvalidChars: true,
         proteinSequence: "",
         chromatogramData: undefined
       },

package/src/rotateSequenceDataToPosition.js

@@ -9,7 +9,10 @@ export default function rotateSequenceDataToPosition(
   caretPosition,
   options
 ) {
-  const newSequenceData = tidyUpSequenceData(sequenceData, options);
+  const newSequenceData = tidyUpSequenceData(sequenceData, {
+    doNotRemoveInvalidChars: true,
+    ...options
+  });
 
   //update the sequence
   newSequenceData.sequence = rotateBpsToPosition(