@teselagen/sequence-utils 0.3.37 → 0.3.38-beta.1

package/findOrfsInPlasmid.d.ts

@@ -1,11 +1,2 @@
-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;
-}[];
+import { Orf } from './getOrfsFromSequence';
+export default function findOrfsInPlasmid(sequence: string, circular: boolean, minimumOrfSize: number, useAdditionalOrfStartCodons: boolean, isProteinOrOligo: boolean): Orf[];

package/findSequenceMatches.d.ts

@@ -1 +1,11 @@
-export default function findSequenceMatches(sequence: any, searchString: any, options?: {}): any[];
+import { Range } from '../../range-utils/src/index.ts';
+export interface FindSequenceMatchesOptions {
+    searchReverseStrand?: boolean;
+    isCircular?: boolean;
+    isAmbiguous?: boolean;
+    isProteinSequence?: boolean;
+    isProteinSearch?: boolean;
+}
+export default function findSequenceMatches(sequence: string, searchString: string, options?: FindSequenceMatchesOptions): (Range & {
+    bottomStrand?: boolean;
+})[];

package/generateAnnotations.d.ts

@@ -1,2 +1,3 @@
+import { Annotation } from './types';
+declare function generateAnnotations(numberOfAnnotationsToGenerate: number, start: number, end: number, maxLength: number): Annotation[];
 export default generateAnnotations;
-declare function generateAnnotations(numberOfAnnotationsToGenerate: any, start: any, end: any, maxLength: any): {};

package/generateSequenceData.d.ts

@@ -1,14 +1,9 @@
+import { SequenceData } from './types';
 export default function generateSequenceData({ isProtein, sequenceLength, numFeatures, numParts, numPrimers, numTranslations }?: {
-    sequenceLength?: number | undefined;
-}): {
-    circular: boolean;
-    name: string;
-    description: string;
-    isProtein: any;
-    sequence: string | false;
-    proteinSequence: any;
-    translations: {} | undefined;
-    features: {};
-    primers: {} | undefined;
-    parts: {};
-};
+    isProtein?: boolean;
+    sequenceLength?: number;
+    numFeatures?: number;
+    numParts?: number;
+    numPrimers?: number;
+    numTranslations?: number;
+}): SequenceData;

package/getAllInsertionsInSeqReads.d.ts

@@ -1 +1,11 @@
-export default function getAllInsertionsInSeqReads(seqReads: any): any[];
+export interface SeqRead {
+    name: string;
+    seq: string;
+    pos: number;
+    cigar: string;
+}
+export interface InsertionInfo {
+    bpPos: number;
+    number: number;
+}
+export default function getAllInsertionsInSeqReads(seqReads: SeqRead[]): InsertionInfo[];

package/getAminoAcidDataForEachBaseOfDna.d.ts

@@ -1,3 +1,4 @@
+import { Range } from '../../range-utils/src/index.ts';
 /**
  * @private
  * Gets aminoAcid data, including position in string and position in codon
@@ -10,21 +11,21 @@
         positionInCodon:
       }]
  */
-export default function getAminoAcidDataForEachBaseOfDna(originalSequenceString: any, forward: boolean, optionalSubrangeRange: any, isProteinSequence: boolean): ({
+export default function getAminoAcidDataForEachBaseOfDna(originalSequenceString: string, forward: boolean, optionalSubrangeRange: Range | null, isProteinSequence: boolean): ({
     aminoAcid: any;
     positionInCodon: number;
     aminoAcidIndex: number;
-    sequenceIndex: any;
+    sequenceIndex: number;
     codonRange: {
-        start: any;
-        end: any;
+        start: number;
+        end: number;
     };
     fullCodon: boolean;
 } | {
     aminoAcid: null;
     positionInCodon: null;
     aminoAcidIndex: null;
-    sequenceIndex: any;
+    sequenceIndex: number;
     codonRange: null;
     fullCodon: null;
 })[];

package/getAminoAcidFromSequenceTriplet.d.ts

@@ -1 +1 @@
-export default function getAminoAcidFromSequenceTriplet(sequenceString: any): any;
+export default function getAminoAcidFromSequenceTriplet(sequenceString: string): any;

package/getAminoAcidStringFromSequenceString.d.ts

@@ -1 +1,3 @@
-export default function getAminoAcidStringFromSequenceString(sequenceString: any, { doNotExcludeAsterisk }?: {}): string;
+export default function getAminoAcidStringFromSequenceString(sequenceString: string, options?: {
+    doNotExcludeAsterisk?: boolean;
+}): string;

package/getCodonRangeForAASliver.d.ts

@@ -1,4 +1,3 @@
-export default function getCodonRangeForAASliver(aminoAcidPositionInSequence: any, aminoAcidSliver: any, AARepresentationOfTranslation: any, relativeAAPositionInTranslation: any): {
-    start: any;
-    end: any;
-};
+import { AminoAcidData } from './types';
+import { Range } from '../../range-utils/src/index.ts';
+export default function getCodonRangeForAASliver(aminoAcidPositionInSequence: number, aminoAcidSliver: AminoAcidData, AARepresentationOfTranslation: AminoAcidData[], relativeAAPositionInTranslation: number): Range;

package/getComplementAminoAcidStringFromSequenceString.d.ts

@@ -1 +1 @@
-export default function getComplementAminoAcidStringFromSequenceString(sequenceString: any): string;
+export default function getComplementAminoAcidStringFromSequenceString(sequenceString: string): string;

package/getComplementSequenceAndAnnotations.d.ts

@@ -1 +1,5 @@
-export default function getComplementSequenceAndAnnotations(pSeqObj: any, options?: {}): any;
+import { SequenceData, Range } from './types';
+export default function getComplementSequenceAndAnnotations(pSeqObj: SequenceData, options?: {
+    range?: Range;
+    [key: string]: unknown;
+}): SequenceData;

package/getComplementSequenceString.d.ts

@@ -1 +1 @@
-export default function getComplementSequenceString(sequence: any, isRna: any): string;
+export default function getComplementSequenceString(sequence: string, isRna?: boolean): string;

package/getCutsiteType.d.ts

@@ -1 +1,2 @@
-export default function getCutsiteType(restrictionEnzyme: any): "blunt" | "5' overhang" | "3' overhang";
+import { RestrictionEnzyme } from './types';
+export default function getCutsiteType(restrictionEnzyme: RestrictionEnzyme): string;

package/getCutsitesFromSequence.d.ts

@@ -1 +1,2 @@
-export default function getCutsitesFromSequence(sequence: any, circular: any, restrictionEnzymes: any): {};
+import { CutSite, RestrictionEnzyme } from './types';
+export default function getCutsitesFromSequence(sequence: string, circular: boolean, contextEnzymes: RestrictionEnzyme[]): Record<string, CutSite[]>;

package/getDegenerateDnaStringFromAAString.d.ts

@@ -1 +1 @@
-export default function getDegenerateDnaStringFromAAString(aaString: any): any;
+export default function getDegenerateDnaStringFromAAString(aaString: string): string;

package/getDegenerateRnaStringFromAAString.d.ts

@@ -1 +1 @@
-export default function getDegenerateRnaStringFromAAString(aaString: any): any;
+export default function getDegenerateRnaStringFromAAString(aaString: string): string;

package/getDigestFragmentsForCutsites.d.ts

@@ -1 +1,4 @@
-export default function getDigestFragmentsForCutsites(sequenceLength: any, circular: any, cutsites: any, opts?: {}): any[];
+import { CutSite, DigestFragment } from './types';
+export default function getDigestFragmentsForCutsites(sequenceLength: number, circular: boolean, cutsites: CutSite[], opts?: {
+    computePartialDigests?: boolean;
+}): DigestFragment[];

package/getDigestFragmentsForRestrictionEnzymes.d.ts

@@ -1 +1,8 @@
-export default function getDigestFragmentsForRestrictionEnzymes(sequence: any, circular: any, restrictionEnzymeOrEnzymes: any, opts: any): any[];
+import { RestrictionEnzyme } from './types';
+export default function getDigestFragmentsForRestrictionEnzymes(sequence: string, circular: boolean, contextEnzymes: RestrictionEnzyme[] | RestrictionEnzyme, options?: {
+    computePartialDigest?: boolean;
+    computePartialDigests?: boolean;
+    computeDigestDisabled?: boolean;
+    computePartialDigestDisabled?: boolean;
+    includeOverAndUnderHangs?: boolean;
+}): import('./types').DigestFragment[];

package/getInsertBetweenVals.d.ts

@@ -1 +1,2 @@
-export default function getInsertBetweenVals(caretPosition: any, selectionLayer: any, sequenceLength: any): any[];
+import { Range } from '../../range-utils/src/index.ts';
+export default function getInsertBetweenVals(caretPosition: number, selectionLayer: Range, sequenceLength: number): [number, number];

package/getLeftAndRightOfSequenceInRangeGivenPosition.d.ts

@@ -1,4 +1,5 @@
-export default function getLeftAndRightOfSequenceInRangeGivenPosition(range: any, position: any, sequence: any): {
+import { Range } from '../../range-utils/src/index.ts';
+export default function getLeftAndRightOfSequenceInRangeGivenPosition(range: Range, position: number, sequence: string): {
     leftHandSide: string;
     rightHandSide: string;
 };

package/getOrfsFromSequence.d.ts

@@ -1,3 +1,18 @@
+import { Annotation } from './types';
+interface GetOrfsOptions {
+    sequence: string;
+    minimumOrfSize: number;
+    forward: boolean;
+    circular?: boolean;
+    useAdditionalOrfStartCodons?: boolean;
+}
+export interface Orf extends Annotation {
+    internalStartCodonIndices: number[];
+    frame: number;
+    isOrf: boolean;
+    remove?: boolean;
+    length: number;
+}
 /**
  * @private
  * Finds ORFs in a given DNA forward in a given frame.
@@ -7,14 +22,5 @@
  * forward - Should we find forward facing orfs or reverse facing orfs
  * return - The list of ORFs found.
  */
-export default function getOrfsFromSequence(options: any): {
-    start: number;
-    end: number;
-    length: number;
-    internalStartCodonIndices: never[];
-    frame: number;
-    forward: any;
-    annotationTypePlural: string;
-    isOrf: boolean;
-    id: any;
-}[];
+export default function getOrfsFromSequence(options: GetOrfsOptions): Orf[];
+export {};

package/getOverlapBetweenTwoSequences.d.ts

@@ -1,3 +1,4 @@
+import { Range } from '../../range-utils/src/index.ts';
 /**
  * This function gets the overlapping of one sequence to another based on sequence equality.
  *
@@ -6,4 +7,4 @@
  * @param  {object} options            optional
  * @return {object || null}            null if no overlap exists or a range object with .start and .end properties
  */
-export default function getOverlapBetweenTwoSequences(sequenceToFind: string, sequenceToSearchIn: string): object;
+export default function getOverlapBetweenTwoSequences(sequenceToFind: string, sequenceToSearchIn: string): Range | null;

package/getPossiblePartsFromSequenceAndEnzymes.d.ts

@@ -1 +1,18 @@
-export default function getPossiblePartsFromSequenceAndEnzyme(seqData: any, restrictionEnzymes: any): any[];
+import { CutSite, RestrictionEnzyme, SequenceData } from './types';
+export interface PartBetweenEnzymes {
+    start: number;
+    start1Based: number;
+    end: number;
+    end1Based: number;
+    firstCut: CutSite;
+    firstCutOffset: number;
+    firstCutOverhang: string;
+    firstCutOverhangTop: string;
+    firstCutOverhangBottom: string;
+    secondCut: CutSite;
+    secondCutOffset: number;
+    secondCutOverhang: string;
+    secondCutOverhangTop: string;
+    secondCutOverhangBottom: string;
+}
+export default function getPossiblePartsFromSequenceAndEnzymes(seqData: SequenceData, restrictionEnzymes: RestrictionEnzyme | RestrictionEnzyme[]): PartBetweenEnzymes[];

package/getReverseAminoAcidStringFromSequenceString.d.ts

@@ -1 +1 @@
-export default function getReverseAminoAcidStringFromSequenceString(sequenceString: any): string;
+export default function getReverseAminoAcidStringFromSequenceString(sequenceString: string): string;

package/getReverseComplementAminoAcidStringFromSequenceString.d.ts

@@ -1 +1 @@
-export default function getReverseComplementAminoAcidStringFromSequenceString(sequenceString: any): string;
+export default function getReverseComplementAminoAcidStringFromSequenceString(sequenceString: string): string;

package/getReverseComplementAnnotation.d.ts

@@ -1 +1,11 @@
-export default function getReverseComplementAnnotation(annotation: any, sequenceLength: any): any;
+import { Annotation } from './types';
+export default function getReverseComplementAnnotation(annotation: Annotation, sequenceLength: number): Annotation & {
+    locations?: {
+        start: number;
+        end: number;
+    }[] | undefined;
+    start: number;
+    end: number;
+    forward: boolean;
+    strand: number;
+};

package/getReverseComplementSequenceAndAnnotations.d.ts

@@ -1 +1,5 @@
-export default function getReverseComplementSequenceAndAnnoations(pSeqObj: any, options?: {}): any;
+import { SequenceData, Range } from './types';
+export default function getReverseComplementSequenceAndAnnoations(pSeqObj: SequenceData, options?: {
+    range?: Range;
+    [key: string]: unknown;
+}): SequenceData;

package/getReverseComplementSequenceString.d.ts

@@ -1 +1 @@
-export default function getReverseComplementSequenceString(sequence: any): string;
+export default function getReverseComplementSequenceString(sequence: string): string;

package/getReverseSequenceString.d.ts

@@ -1 +1 @@
-export default function getReverseSequenceString(sequence: any): string;
+export default function getReverseSequenceString(sequence: string): string;

package/getSequenceDataBetweenRange.d.ts

@@ -1 +1,9 @@
-export default function getSequenceDataBetweenRange(seqData: any, range: any, options?: {}): any;
+import { Range } from '../../range-utils/src/index.ts';
+import { SequenceData } from './types';
+interface GetSequenceDataBetweenRangeOptions {
+    exclude?: Record<string, boolean>;
+    excludePartial?: Record<string, boolean>;
+    [key: string]: unknown;
+}
+export default function getSequenceDataBetweenRange(seqData: SequenceData, range: Range | null, options?: GetSequenceDataBetweenRangeOptions): SequenceData;
+export {};

package/getVirtualDigest.d.ts

@@ -1,13 +1,14 @@
+import { CutSite, DigestFragment } from './types';
 export default function getVirtualDigest({ cutsites, sequenceLength, isCircular, computePartialDigest, computePartialDigestDisabled, computeDigestDisabled }: {
-    cutsites: any;
-    sequenceLength: any;
-    isCircular: any;
-    computePartialDigest: any;
-    computePartialDigestDisabled: any;
-    computeDigestDisabled: any;
+    cutsites: CutSite[];
+    sequenceLength: number;
+    isCircular: boolean;
+    computePartialDigest?: boolean;
+    computePartialDigestDisabled?: boolean;
+    computeDigestDisabled?: boolean;
 }): {
-    computePartialDigestDisabled: any;
-    computeDigestDisabled: any;
-    fragments: any[];
-    overlappingEnzymes: any[];
+    computePartialDigestDisabled: boolean | undefined;
+    computeDigestDisabled: boolean | undefined;
+    fragments: DigestFragment[];
+    overlappingEnzymes: DigestFragment[];
 };

package/guessIfSequenceIsDnaAndNotProtein.d.ts

@@ -1 +1,5 @@
-export default function guessIfSequenceIsDnaAndNotProtein(seq: any, options?: {}): boolean;
+export default function guessIfSequenceIsDnaAndNotProtein(seq: string, options?: {
+    threshold?: number;
+    loose?: boolean;
+    dnaLetters?: string[];
+}): boolean;