@teselagen/sequence-utils 0.3.38-beta.3 → 0.3.42

package/DNAComplementMap.d.ts

@@ -1,3 +1,4 @@
+export default DNAComplementMap;
 declare const DNAComplementMap: {
     ".": string;
     a: string;
@@ -27,4 +28,3 @@ declare const DNAComplementMap: {
     b: string;
     B: string;
 };
-export default DNAComplementMap;

package/README.md

@@ -64,15 +64,9 @@ Make sure they pass by running `npm test`
 
 Commit and push all changes first (make sure tests are passing!)
 
-### Teselagen collaborators:
+# Publishing
 
-Commit and push all changes
-Sign into npm using the teselagen npm account (npm whoami)
-
-```
-npm version patch|minor|major
-npm publish
-```
+See the [README](../README.md)
 
 ### Outside collaborators:
 

package/addGapsToSeqReads.d.ts

@@ -1,17 +1,4 @@
-interface SeqRead {
-    name: string;
-    seq: string;
-    pos: number;
-    cigar: string;
-    reversed?: boolean;
-}
-export default function addGapsToSeqReads(refSeq: {
-    name: string;
-    sequence: string;
-}, seqReads: SeqRead[]): {
-    name: string;
-    sequence: string;
-    reversed?: boolean;
-    cigar?: string;
+export default function addGapsToSeqReads(refSeq: any, seqReads: any): {
+    name: any;
+    sequence: any;
 }[];
-export {};

package/adjustAnnotationsToInsert.d.ts

@@ -1,2 +1 @@
-import { Annotation } from './types';
-export default function adjustAnnotationsToInsert(annotationsToBeAdjusted: Record<string, Annotation> | Annotation[], insertStart: number, insertLength: number): boolean[];
+export default function adjustAnnotationsToInsert(annotationsToBeAdjusted: any, insertStart: any, insertLength: any): any[];

package/adjustBpsToReplaceOrInsert.d.ts

@@ -1,2 +1 @@
-import { Range } from '../../range-utils/src/index.ts';
-export default function adjustBpsToReplaceOrInsert(bpString: string, insertString: string | undefined, caretPositionOrRange: number | Range): string;
+export default function adjustBpsToReplaceOrInsert(bpString: any, insertString: string | undefined, caretPositionOrRange: any): any;

package/aliasedEnzymesByName.d.ts

@@ -1,38 +1,2 @@
-declare const aliasedEnzymes: ({
-    aliases: string[];
-    site: string;
-    forwardRegex: string;
-    reverseRegex: string;
-    topSnipOffset: number;
-    bottomSnipOffset: number;
-    isType2S?: undefined;
-    cutType?: undefined;
-    usForward?: undefined;
-    usReverse?: undefined;
-} | {
-    aliases: string[];
-    site: string;
-    forwardRegex: string;
-    reverseRegex: string;
-    topSnipOffset: number;
-    bottomSnipOffset: number;
-    isType2S: boolean;
-    cutType?: undefined;
-    usForward?: undefined;
-    usReverse?: undefined;
-} | {
-    aliases: string[];
-    isType2S: boolean;
-    site: string;
-    forwardRegex: string;
-    reverseRegex: string;
-    topSnipOffset: number;
-    bottomSnipOffset: number;
-    cutType: number;
-    usForward: number;
-    usReverse: number;
-})[];
-declare const aliasedEnzymesByName: Record<string, (typeof aliasedEnzymes)[number] & {
-    name: string;
-}>;
 export default aliasedEnzymesByName;
+declare const aliasedEnzymesByName: {};

package/aminoAcidToDegenerateDnaMap.d.ts

@@ -1,2 +1,32 @@
-declare const aminoAcidToDegenerateDnaMap: Record<string, string>;
 export default aminoAcidToDegenerateDnaMap;
+declare const aminoAcidToDegenerateDnaMap: {
+    "-": string;
+    ".": string;
+    "*": string;
+    a: string;
+    b: string;
+    c: string;
+    d: string;
+    e: string;
+    f: string;
+    g: string;
+    h: string;
+    i: string;
+    j: string;
+    k: string;
+    l: string;
+    m: string;
+    n: string;
+    o: string;
+    p: string;
+    q: string;
+    r: string;
+    s: string;
+    t: string;
+    u: string;
+    v: string;
+    w: string;
+    x: string;
+    y: string;
+    z: string;
+};

package/aminoAcidToDegenerateRnaMap.d.ts

@@ -1,3 +1,4 @@
+export default aminoAcidToDegenerateRnaMap;
 declare const aminoAcidToDegenerateRnaMap: {
     "-": string;
     ".": string;
@@ -29,4 +30,3 @@ declare const aminoAcidToDegenerateRnaMap: {
     y: string;
     z: string;
 };
-export default aminoAcidToDegenerateRnaMap;

package/annotateSingleSeq.d.ts

@@ -1,8 +1,7 @@
-import { SequenceData } from './types';
+export default annotateSingleSeq;
 declare function annotateSingleSeq({ fullSeq, searchSeq }: {
-    fullSeq: SequenceData;
-    searchSeq: SequenceData;
+    fullSeq: any;
+    searchSeq: any;
 }): {
-    matches: import('./types').Annotation[] | Record<string, string[]>;
+    matches: any;
 };
-export default annotateSingleSeq;

package/annotationTypes.d.ts

@@ -1,2 +1,2 @@
-export declare const annotationTypes: string[];
-export declare const modifiableTypes: string[];
+export const annotationTypes: string[];
+export const modifiableTypes: string[];

package/autoAnnotate.d.ts

@@ -1,17 +1,8 @@
-import { Annotation } from './types';
-declare function autoAnnotate({ seqsToAnnotateById, annotationsToCheckById, compareName, warnIfMoreThan }: {
-    seqsToAnnotateById: Record<string, {
-        sequence: string;
-        annotations: Annotation[];
-        circular?: boolean;
-    }>;
-    annotationsToCheckById: Record<string, {
-        sequence: string;
-        id: string;
-    }>;
-    compareName?: boolean;
-    warnIfMoreThan?: number;
-}): Record<string, Annotation[] | Record<string, string[]>>;
-declare function convertApELikeRegexToRegex(regString?: string): string;
-declare function convertProteinSeqToDNAIupac(sequence: string): string;
-export { convertProteinSeqToDNAIupac, convertApELikeRegexToRegex, autoAnnotate };
+export function convertProteinSeqToDNAIupac(sequence: any): string;
+export function convertApELikeRegexToRegex(regString?: string): string;
+export function autoAnnotate({ seqsToAnnotateById, annotationsToCheckById, compareName, warnIfMoreThan }: {
+    seqsToAnnotateById: any;
+    annotationsToCheckById: any;
+    compareName: any;
+    warnIfMoreThan: any;
+}): {};

package/bioData.d.ts

@@ -1,10 +1,58 @@
-export declare const protein_letters = "ACDEFGHIKLMNPQRSTVWY";
-export declare const protein_letters_withUandX = "ACDEFGHIKLMNPQRSTVWYUX";
-export declare const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
-export declare const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
-export declare const unambiguous_dna_letters = "GATC";
-export declare const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
-export declare const unambiguous_rna_letters = "GAUC";
-export declare const extended_dna_letters = "GATCBDSW";
-export declare const ambiguous_dna_values: Record<string, string>;
-export declare const extended_protein_values: Record<string, string>;
+export const protein_letters: "ACDEFGHIKLMNPQRSTVWY";
+export const protein_letters_withUandX: "ACDEFGHIKLMNPQRSTVWYUX";
+export const extended_protein_letters: "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
+export const ambiguous_dna_letters: "GATCRYWSMKHBVDN";
+export const unambiguous_dna_letters: "GATC";
+export const ambiguous_rna_letters: "GAUCRYWSMKHBVDN";
+export const unambiguous_rna_letters: "GAUC";
+export const extended_dna_letters: "GATCBDSW";
+export const ambiguous_dna_values: {
+    ".": string;
+    A: string;
+    C: string;
+    G: string;
+    T: string;
+    M: string;
+    R: string;
+    W: string;
+    S: string;
+    Y: string;
+    K: string;
+    V: string;
+    H: string;
+    D: string;
+    B: string;
+    X: string;
+    N: string;
+};
+export const extended_protein_values: {
+    A: string;
+    B: string;
+    C: string;
+    D: string;
+    E: string;
+    F: string;
+    G: string;
+    H: string;
+    I: string;
+    J: string;
+    K: string;
+    L: string;
+    M: string;
+    N: string;
+    O: string;
+    P: string;
+    Q: string;
+    R: string;
+    S: string;
+    T: string;
+    U: string;
+    V: string;
+    W: string;
+    X: string;
+    Y: string;
+    Z: string;
+    "*": string;
+    ".": string;
+    "-": string;
+};

package/calculateEndStability.d.ts

@@ -13,4 +13,4 @@
  * @returns {number} - Delta G (kcal/mol) for the last 5 bases at 3' end
  * @throws {Error} Invalid sequence or too short.
  */
-export default function calculateEndStability(sequence: string): number | string;
+export default function calculateEndStability(sequence: string): number;

package/calculateNebTa.d.ts

@@ -1,6 +1 @@
-interface NebTaOptions {
-    monovalentCationConc?: number;
-    polymerase?: string;
-}
-export default function calculateNebTa(sequences: string[], primerConc: number, { monovalentCationConc, polymerase }?: NebTaOptions): number | string;
-export {};
+export default function calculateNebTa(sequences: any, primerConc: any, { monovalentCationConc, polymerase }?: {}): any;

package/calculateNebTm.d.ts

@@ -1,6 +1,4 @@
-interface NebTmOptions {
-    monovalentCationConc?: number;
-    primerConc?: number;
-}
-export default function calculateNebTm(sequence: string, { monovalentCationConc, primerConc }?: NebTmOptions): number | string;
-export {};
+export default function calculateNebTm(sequence: any, { monovalentCationConc, primerConc }?: {
+    monovalentCationConc?: number | undefined;
+    primerConc?: number | undefined;
+}): string | number;

package/calculatePercentGC.d.ts

@@ -1 +1 @@
-export default function calculatePercentGC(bps: string): number;
+export default function calculatePercentGC(bps: any): number;

package/calculateSantaLuciaTm.d.ts

@@ -1,36 +1,10 @@
-/**
- * Primer3 Melting Temperature Calculator
- *
- * Implements the melting temperature calculation algorithm from Primer3
- * based on the documentation at https://primer3.ut.ee/primer3web_help.htm
- *
- * Uses SantaLucia (1998) nearest-neighbor thermodynamics method with
- * fixed Primer3 custom parameters:
- * - Formula: SantaLucia (1998)
- * - Salt correction: SantaLucia (1998)
- * - Monovalent salt: 50.0 mM
- * - Divalent salt: 1.5 mM
- * - dNTP concentration: 0.6 mM
- * - DNA concentration: 50.0 nM
- *
- * References:
- * - SantaLucia JR (1998) "A unified view of polymer, dumbbell and
- *   oligonucleotide DNA nearest-neighbor thermodynamics",
- *   Proc Natl Acad Sci 95:1460-65
- */
-export interface SantaLuciaParams {
-    dH: number;
-    dS: number;
-}
-export declare const SANTA_LUCIA_NN: Record<string, SantaLuciaParams>;
-export declare const SANTA_LUCIA_INIT: Record<string, SantaLuciaParams>;
 /**
  * Validate DNA sequence
  *
  * @param {string} sequence - DNA sequence
  * @returns {boolean} - True if valid
  */
-export declare function isValidSequence(sequence: string): boolean;
+export function isValidSequence(sequence: string): boolean;
 /**
  * Calculate melting temperature using SantaLucia (1998) method
  *
@@ -38,4 +12,116 @@ export declare function isValidSequence(sequence: string): boolean;
  * @returns {number} - Melting temperature in Celsius
  * @throws {Error} Invalid sequence or too short.
  */
-export default function calculateSantaLuciaTm(sequence: string): number | string;
+export default function calculateSantaLuciaTm(sequence: string): number;
+export namespace SANTA_LUCIA_NN {
+    namespace AA {
+        let dH: number;
+        let dS: number;
+    }
+    namespace TT {
+        let dH_1: number;
+        export { dH_1 as dH };
+        let dS_1: number;
+        export { dS_1 as dS };
+    }
+    namespace AT {
+        let dH_2: number;
+        export { dH_2 as dH };
+        let dS_2: number;
+        export { dS_2 as dS };
+    }
+    namespace TA {
+        let dH_3: number;
+        export { dH_3 as dH };
+        let dS_3: number;
+        export { dS_3 as dS };
+    }
+    namespace CA {
+        let dH_4: number;
+        export { dH_4 as dH };
+        let dS_4: number;
+        export { dS_4 as dS };
+    }
+    namespace TG {
+        let dH_5: number;
+        export { dH_5 as dH };
+        let dS_5: number;
+        export { dS_5 as dS };
+    }
+    namespace GT {
+        let dH_6: number;
+        export { dH_6 as dH };
+        let dS_6: number;
+        export { dS_6 as dS };
+    }
+    namespace AC {
+        let dH_7: number;
+        export { dH_7 as dH };
+        let dS_7: number;
+        export { dS_7 as dS };
+    }
+    namespace CT {
+        let dH_8: number;
+        export { dH_8 as dH };
+        let dS_8: number;
+        export { dS_8 as dS };
+    }
+    namespace AG {
+        let dH_9: number;
+        export { dH_9 as dH };
+        let dS_9: number;
+        export { dS_9 as dS };
+    }
+    namespace GA {
+        let dH_10: number;
+        export { dH_10 as dH };
+        let dS_10: number;
+        export { dS_10 as dS };
+    }
+    namespace TC {
+        let dH_11: number;
+        export { dH_11 as dH };
+        let dS_11: number;
+        export { dS_11 as dS };
+    }
+    namespace CG {
+        let dH_12: number;
+        export { dH_12 as dH };
+        let dS_12: number;
+        export { dS_12 as dS };
+    }
+    namespace GC {
+        let dH_13: number;
+        export { dH_13 as dH };
+        let dS_13: number;
+        export { dS_13 as dS };
+    }
+    namespace GG {
+        let dH_14: number;
+        export { dH_14 as dH };
+        let dS_14: number;
+        export { dS_14 as dS };
+    }
+    namespace CC {
+        let dH_15: number;
+        export { dH_15 as dH };
+        let dS_15: number;
+        export { dS_15 as dS };
+    }
+}
+export namespace SANTA_LUCIA_INIT {
+    export namespace GC_1 {
+        let dH_16: number;
+        export { dH_16 as dH };
+        let dS_16: number;
+        export { dS_16 as dS };
+    }
+    export { GC_1 as GC };
+    export namespace AT_1 {
+        let dH_17: number;
+        export { dH_17 as dH };
+        let dS_17: number;
+        export { dS_17 as dS };
+    }
+    export { AT_1 as AT };
+}

package/calculateTm.d.ts

@@ -1,14 +1,2 @@
-/**
- * DNA melting temperature calculator.
- * @author Nick Elsbree
- * @author Zinovii Dmytriv (original author)
- */
-interface CalculateTemperatureOptions {
-    type?: "breslauer" | "sugimoto" | "unified";
-    A?: number;
-    R?: number;
-    primerConc?: number;
-    monovalentCationConc?: number;
-}
-declare const _default: (_sequence: string, { type, A, R, primerConc, monovalentCationConc }?: CalculateTemperatureOptions) => number;
+declare function _default(_sequence: any, { type, A, R, primerConc, monovalentCationConc }?: {}): number;
 export default _default;

package/computeDigestFragments.d.ts

@@ -1,33 +1,27 @@
-import { CutSite, DigestFragment, RestrictionEnzyme } from './types';
-export interface ComputeDigestFragmentsParams {
-    cutsites: CutSite[];
-    sequenceLength: number;
-    circular: boolean;
-    includeOverAndUnderHangs?: boolean;
-    computePartialDigest?: boolean;
-    computeDigestDisabled?: boolean;
-    computePartialDigestDisabled?: boolean;
-    selectionLayerUpdate?: (params: {
-        start: number;
-        end: number;
-        name: string;
-    }) => void;
-    updateSelectedFragment?: (id: string) => void;
-}
-export declare function computeDigestFragments({ cutsites, sequenceLength, circular, includeOverAndUnderHangs, computePartialDigest, computeDigestDisabled, computePartialDigestDisabled, selectionLayerUpdate, updateSelectedFragment }: ComputeDigestFragmentsParams): {
-    computePartialDigestDisabled: boolean | undefined;
-    computeDigestDisabled: boolean | undefined;
-    fragments: DigestFragment[];
-    overlappingEnzymes: DigestFragment[];
+export function computeDigestFragments({ cutsites, sequenceLength, circular, includeOverAndUnderHangs, computePartialDigest, computeDigestDisabled, computePartialDigestDisabled, selectionLayerUpdate, updateSelectedFragment }: {
+    cutsites: any;
+    sequenceLength: any;
+    circular: any;
+    includeOverAndUnderHangs: any;
+    computePartialDigest: any;
+    computeDigestDisabled: any;
+    computePartialDigestDisabled: any;
+    selectionLayerUpdate: any;
+    updateSelectedFragment: any;
+}): {
+    computePartialDigestDisabled: any;
+    computeDigestDisabled: any;
+    fragments: any[];
+    overlappingEnzymes: any[];
 };
-export declare function getDigestFragsForSeqAndEnzymes({ sequence, circular, enzymes, includeOverAndUnderHangs }: {
-    sequence: string;
-    circular: boolean;
-    enzymes: RestrictionEnzyme[];
-    includeOverAndUnderHangs?: boolean;
+export function getDigestFragsForSeqAndEnzymes({ sequence, circular, enzymes, includeOverAndUnderHangs }: {
+    sequence: any;
+    circular: any;
+    enzymes: any;
+    includeOverAndUnderHangs: any;
 }): {
-    computePartialDigestDisabled: boolean | undefined;
-    computeDigestDisabled: boolean | undefined;
-    fragments: DigestFragment[];
-    overlappingEnzymes: DigestFragment[];
+    computePartialDigestDisabled: any;
+    computeDigestDisabled: any;
+    fragments: any[];
+    overlappingEnzymes: any[];
 };

package/condensePairwiseAlignmentDifferences.d.ts

@@ -1 +1 @@
-export default function condensePairwiseAlignmentDifferences(referenceSeq: string, alignedSeq: string): string;
+export default function condensePairwiseAlignmentDifferences(referenceSeq: any, alignedSeq: any): string;

package/convertAACaretPositionOrRangeToDna.d.ts

@@ -1,2 +1 @@
-import { Range } from './types';
-export default function convertAACaretPositionOrRangeToDna(rangeOrCaret: Range | number): Range | number;
+export default function convertAACaretPositionOrRangeToDna(rangeOrCaret: any): any;

package/convertDnaCaretPositionOrRangeToAA.d.ts

@@ -1,2 +1 @@
-import { Range } from './types';
-export default function convertDnaCaretPositionOrRangeToAA(rangeOrCaret: Range | number): Range | number;
+export default function convertDnaCaretPositionOrRangeToAA(rangeOrCaret: any): any;

package/cutSequenceByRestrictionEnzyme.d.ts

@@ -1,2 +1 @@
-import { CutSite, RestrictionEnzyme } from './types';
-export default function cutSequenceByRestrictionEnzyme(pSequence: string, circular: boolean, restrictionEnzyme: RestrictionEnzyme): CutSite[];
+export default function cutSequenceByRestrictionEnzyme(pSequence: any, circular: any, restrictionEnzyme: any): any[];

package/defaultEnzymesByName.d.ts

@@ -1,3 +1,2 @@
-import { RestrictionEnzyme } from './types';
-declare const defaultEnzymesByName: Record<string, RestrictionEnzyme>;
 export default defaultEnzymesByName;
+declare const defaultEnzymesByName: {};

package/degenerateDnaToAminoAcidMap.d.ts

@@ -1,2 +1,2 @@
-declare const degenerateDnaToAminoAcidMap: import('lodash').Dictionary<string>;
 export default degenerateDnaToAminoAcidMap;
+declare const degenerateDnaToAminoAcidMap: import('lodash').Dictionary<string>;

package/degenerateRnaToAminoAcidMap.d.ts

@@ -1,2 +1,2 @@
-declare const degenerateRnaToAminoAcidMap: import('lodash').Dictionary<string>;
 export default degenerateRnaToAminoAcidMap;
+declare const degenerateRnaToAminoAcidMap: import('lodash').Dictionary<string>;

package/deleteSequenceDataAtRange.d.ts

@@ -1,2 +1 @@
-import { SequenceData, Range } from './types';
-export default function deleteSequenceDataAtRange(sequenceData: SequenceData, range: Range): SequenceData;
+export default function deleteSequenceDataAtRange(sequenceData: any, range: any): any;

package/diffUtils.d.ts

@@ -1,9 +1,7 @@
-import { Delta } from 'jsondiffpatch';
-import { SequenceData } from './types';
-interface DiffOptions {
-    ignoreKeys?: string[];
-}
-declare const getDiffFromSeqs: (oldData: SequenceData, newData: SequenceData, { ignoreKeys }?: DiffOptions) => Delta | undefined;
-declare const patchSeqWithDiff: (oldData: SequenceData, diffData: Delta, { ignoreKeys }?: DiffOptions) => SequenceData;
-declare const reverseSeqDiff: (diffData: Delta) => Delta | undefined;
-export { getDiffFromSeqs, patchSeqWithDiff, reverseSeqDiff };
+export function getDiffFromSeqs(oldData: any, newData: any, { ignoreKeys }?: {
+    ignoreKeys?: never[] | undefined;
+}): import('jsondiffpatch').Delta;
+export function patchSeqWithDiff(oldData: any, diff: any, { ignoreKeys }?: {
+    ignoreKeys?: never[] | undefined;
+}): unknown;
+export function reverseSeqDiff(diff: any): import('jsondiffpatch').Delta;

package/doesEnzymeChopOutsideOfRecognitionSite.d.ts

@@ -1,2 +1 @@
-import { RestrictionEnzyme } from './types';
-export default function doesEnzymeChopOutsideOfRecognitionSite(enzyme: RestrictionEnzyme): boolean;
+export default function doesEnzymeChopOutsideOfRecognitionSite(enzyme: any): boolean;

package/featureTypesAndColors.d.ts

@@ -1,21 +1,8 @@
-interface FeatureType {
+export function getGenbankFeatureToColorMap(): {};
+export const genbankFeatureTypes: {
     name: string;
     color: string;
-    isHidden?: boolean;
-    isGenbankStandardType?: boolean;
-    isOverridden?: boolean;
-    isCustomType?: boolean;
-}
-declare const genbankFeatureTypes: FeatureType[];
-declare const getMergedFeatureMap: () => Record<string, FeatureType>;
-declare const getFeatureToColorMap: ({ includeHidden }?: {
-    includeHidden?: boolean;
-}) => Record<string, string>;
-declare const getFeatureTypes: ({ includeHidden }?: {
-    includeHidden?: boolean;
-}) => string[];
-export { genbankFeatureTypes };
-export declare function getGenbankFeatureToColorMap(): Record<string, string>;
-export { getFeatureToColorMap };
-export { getFeatureTypes };
-export { getMergedFeatureMap };
+}[];
+export function getFeatureToColorMap({ includeHidden }?: {}): {};
+export function getFeatureTypes({ includeHidden }?: {}): any[];
+export function getMergedFeatureMap(): any;

package/filterSequenceString.d.ts

@@ -1,14 +1,10 @@
-interface FilterSequenceStringOptions {
-    additionalValidChars?: string;
-    isOligo?: boolean;
-    name?: string;
-    isProtein?: boolean;
-    isRna?: boolean;
-    isMixedRnaAndDna?: boolean;
-    [key: string]: unknown;
-}
-export default function filterSequenceString(sequenceString?: string, { additionalValidChars, isOligo, name, isProtein, isRna, isMixedRnaAndDna }?: FilterSequenceStringOptions): [string, string[]];
-export declare function getAcceptedChars({ isOligo, isProtein, isRna, isMixedRnaAndDna }?: FilterSequenceStringOptions): string;
-export declare function getReplaceChars({ isOligo, isProtein, isRna, isMixedRnaAndDna }?: FilterSequenceStringOptions): Record<string, string>;
-export declare const filterRnaString: (s: string, o: FilterSequenceStringOptions) => string;
-export {};
+export default function filterSequenceString(sequenceString?: string, { additionalValidChars, isOligo, name, isProtein, isRna, isMixedRnaAndDna, getAcceptedInsertChars }?: {
+    additionalValidChars?: string | undefined;
+}): (string | string[])[];
+export function getAcceptedChars({ isOligo, isProtein, isRna, isMixedRnaAndDna }?: {}): string;
+export function getReplaceChars({ isOligo, isProtein, isRna, isMixedRnaAndDna }?: {}): {
+    t?: undefined;
+} | {
+    t: string;
+};
+export function filterRnaString(s: any, o: any): string | string[];