@teselagen/sequence-utils 0.1.1

package/DNAComplementMap.d.ts

@@ -0,0 +1,30 @@
+export default DNAComplementMap;
+declare const DNAComplementMap: {
+    ".": string;
+    a: string;
+    t: string;
+    u: string;
+    c: string;
+    g: string;
+    A: string;
+    T: string;
+    U: string;
+    C: string;
+    G: string;
+    r: string;
+    R: string;
+    y: string;
+    Y: string;
+    d: string;
+    D: string;
+    h: string;
+    H: string;
+    k: string;
+    K: string;
+    m: string;
+    M: string;
+    v: string;
+    V: string;
+    b: string;
+    B: string;
+};

package/addGapsToSeqReads.d.ts

@@ -0,0 +1,4 @@
+export default function addGapsToSeqReads(refSeq: any, seqReads: any): {
+    name: any;
+    sequence: any;
+}[];

package/adjustAnnotationsToInsert.d.ts

@@ -0,0 +1 @@
+export default function adjustAnnotationsToInsert(annotationsToBeAdjusted: any, insertStart: any, insertLength: any): any[];

package/adjustBpsToReplaceOrInsert.d.ts

@@ -0,0 +1 @@
+export default function adjustBpsToReplaceOrInsert(bpString: any, insertString: string | undefined, caretPositionOrRange: any): any;

package/aliasedEnzymesByName.d.ts

@@ -0,0 +1,2 @@
+export default aliasedEnzymesByName;
+declare const aliasedEnzymesByName: {};

package/aminoAcidToDegenerateDnaMap.d.ts

@@ -0,0 +1,32 @@
+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

@@ -0,0 +1,32 @@
+export default aminoAcidToDegenerateRnaMap;
+declare const aminoAcidToDegenerateRnaMap: {
+    "-": 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/annotateSingleSeq.d.ts

@@ -0,0 +1,7 @@
+export default annotateSingleSeq;
+declare function annotateSingleSeq({ fullSeq, searchSeq }: {
+    fullSeq: any;
+    searchSeq: any;
+}): {
+    matches: any;
+};

package/annotationTypes.d.ts

@@ -0,0 +1,3 @@
+declare const _default: string[];
+export default _default;
+export const modifiableTypes: string[];

package/autoAnnotate.d.ts

@@ -0,0 +1,8 @@
+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

@@ -0,0 +1,396 @@
+export const protein_letters: "ACDEFGHIKLMNPQRSTVWY";
+export const extended_protein_letters: "ACDEFGHIKLMNPQRSTVWYBXZJUO.*-";
+export namespace protein_letters_1to3 {
+    const A: string;
+    const C: string;
+    const D: string;
+    const E: string;
+    const F: string;
+    const G: string;
+    const H: string;
+    const I: string;
+    const K: string;
+    const L: string;
+    const M: string;
+    const N: string;
+    const P: string;
+    const Q: string;
+    const R: string;
+    const S: string;
+    const T: string;
+    const V: string;
+    const W: string;
+    const Y: string;
+    const O: string;
+    const U: string;
+}
+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 ambiguous_rna_values: {
+    ".": string;
+    A: string;
+    C: string;
+    G: string;
+    U: 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 ambiguous_dna_complement: {
+    ".": 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 ambiguous_rna_complement: {
+    ".": string;
+    A: string;
+    C: string;
+    G: string;
+    U: 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 namespace unambiguous_dna_weights {
+    const A_1: number;
+    export { A_1 as A };
+    const C_1: number;
+    export { C_1 as C };
+    const G_1: number;
+    export { G_1 as G };
+    const T_1: number;
+    export { T_1 as T };
+}
+export namespace monoisotopic_unambiguous_dna_weights {
+    const A_2: number;
+    export { A_2 as A };
+    const C_2: number;
+    export { C_2 as C };
+    const G_2: number;
+    export { G_2 as G };
+    const T_2: number;
+    export { T_2 as T };
+}
+export namespace unambiguous_rna_weights {
+    const A_3: number;
+    export { A_3 as A };
+    const C_3: number;
+    export { C_3 as C };
+    const G_3: number;
+    export { G_3 as G };
+    const U_1: number;
+    export { U_1 as U };
+}
+export namespace monoisotopic_unambiguous_rna_weights {
+    const A_4: number;
+    export { A_4 as A };
+    const C_4: number;
+    export { C_4 as C };
+    const G_4: number;
+    export { G_4 as G };
+    const U_2: number;
+    export { U_2 as U };
+}
+export namespace protein_weights {
+    const A_5: number;
+    export { A_5 as A };
+    const C_5: number;
+    export { C_5 as C };
+    const D_1: number;
+    export { D_1 as D };
+    const E_1: number;
+    export { E_1 as E };
+    const F_1: number;
+    export { F_1 as F };
+    const G_5: number;
+    export { G_5 as G };
+    const H_1: number;
+    export { H_1 as H };
+    const I_1: number;
+    export { I_1 as I };
+    const K_1: number;
+    export { K_1 as K };
+    const L_1: number;
+    export { L_1 as L };
+    const M_1: number;
+    export { M_1 as M };
+    const N_1: number;
+    export { N_1 as N };
+    const O_1: number;
+    export { O_1 as O };
+    const P_1: number;
+    export { P_1 as P };
+    const Q_1: number;
+    export { Q_1 as Q };
+    const R_1: number;
+    export { R_1 as R };
+    const S_1: number;
+    export { S_1 as S };
+    const T_3: number;
+    export { T_3 as T };
+    const U_3: number;
+    export { U_3 as U };
+    const V_1: number;
+    export { V_1 as V };
+    const W_1: number;
+    export { W_1 as W };
+    const Y_1: number;
+    export { Y_1 as Y };
+}
+export namespace monoisotopic_protein_weights {
+    const A_6: number;
+    export { A_6 as A };
+    const C_6: number;
+    export { C_6 as C };
+    const D_2: number;
+    export { D_2 as D };
+    const E_2: number;
+    export { E_2 as E };
+    const F_2: number;
+    export { F_2 as F };
+    const G_6: number;
+    export { G_6 as G };
+    const H_2: number;
+    export { H_2 as H };
+    const I_2: number;
+    export { I_2 as I };
+    const K_2: number;
+    export { K_2 as K };
+    const L_2: number;
+    export { L_2 as L };
+    const M_2: number;
+    export { M_2 as M };
+    const N_2: number;
+    export { N_2 as N };
+    const O_2: number;
+    export { O_2 as O };
+    const P_2: number;
+    export { P_2 as P };
+    const Q_2: number;
+    export { Q_2 as Q };
+    const R_2: number;
+    export { R_2 as R };
+    const S_2: number;
+    export { S_2 as S };
+    const T_4: number;
+    export { T_4 as T };
+    const U_4: number;
+    export { U_4 as U };
+    const V_2: number;
+    export { V_2 as V };
+    const W_2: number;
+    export { W_2 as W };
+    const Y_2: number;
+    export { Y_2 as Y };
+}
+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;
+};
+export namespace atom_weights {
+    const H_3: number;
+    export { H_3 as H };
+    const D_3: number;
+    export { D_3 as D };
+    export const He: number;
+    export const Li: number;
+    export const Be: number;
+    export const B: number;
+    const C_7: number;
+    export { C_7 as C };
+    const N_3: number;
+    export { N_3 as N };
+    const O_3: number;
+    export { O_3 as O };
+    const F_3: number;
+    export { F_3 as F };
+    export const Ne: number;
+    export const Na: number;
+    export const Mg: number;
+    export const Al: number;
+    export const Si: number;
+    const P_3: number;
+    export { P_3 as P };
+    const S_3: number;
+    export { S_3 as S };
+    export const Cl: number;
+    export const Ar: number;
+    const K_3: number;
+    export { K_3 as K };
+    export const Ca: number;
+    export const Sc: number;
+    export const Ti: number;
+    const V_3: number;
+    export { V_3 as V };
+    export const Cr: number;
+    export const Mn: number;
+    export const Fe: number;
+    export const Co: number;
+    export const Ni: number;
+    export const Cu: number;
+    export const Zn: number;
+    export const Ga: number;
+    export const Ge: number;
+    export const As: number;
+    export const Se: number;
+    export const Br: number;
+    export const Kr: number;
+    export const Rb: number;
+    export const Sr: number;
+    const Y_3: number;
+    export { Y_3 as Y };
+    export const Zr: number;
+    export const Nb: number;
+    export const Mo: number;
+    export const Tc: number;
+    export const Ru: number;
+    export const Rh: number;
+    export const Pd: number;
+    export const Ag: number;
+    export const Cd: number;
+    export const In: number;
+    export const Sn: number;
+    export const Sb: number;
+    export const Te: number;
+    const I_3: number;
+    export { I_3 as I };
+    export const Xe: number;
+    export const Cs: number;
+    export const Ba: number;
+    export const La: number;
+    export const Ce: number;
+    export const Pr: number;
+    export const Nd: number;
+    export const Pm: number;
+    export const Sm: number;
+    export const Eu: number;
+    export const Gd: number;
+    export const Tb: number;
+    export const Dy: number;
+    export const Ho: number;
+    export const Er: number;
+    export const Tm: number;
+    export const Yb: number;
+    export const Lu: number;
+    export const Hf: number;
+    export const Ta: number;
+    const W_3: number;
+    export { W_3 as W };
+    export const Re: number;
+    export const Os: number;
+    export const Ir: number;
+    export const Pt: number;
+    export const Au: number;
+    export const Hg: number;
+    export const Tl: number;
+    export const Pb: number;
+    export const Bi: number;
+    export const Po: number;
+    export const At: number;
+    export const Rn: number;
+    export const Fr: number;
+    export const Ra: number;
+    export const Ac: number;
+    export const Th: number;
+    export const Pa: number;
+    const U_5: number;
+    export { U_5 as U };
+    export const Np: number;
+    export const Pu: number;
+    export const Am: number;
+    export const Cm: number;
+    export const Bk: number;
+    export const Cf: number;
+    export const Es: number;
+    export const Fm: number;
+    export const Md: number;
+    export const No: number;
+    export const Lr: number;
+    export const Rf: number;
+    export const Db: number;
+    export const Sg: number;
+    export const Bh: number;
+    export const Hs: number;
+    export const Mt: number;
+}

package/calculateNebTa.d.ts

@@ -0,0 +1,4 @@
+export default function calculateNebTa(sequences: any, primerConc: any, { monovalentCationConc, polymerase }?: {
+    monovalentCationConc: any;
+    polymerase: any;
+}): any;

package/calculateNebTm.d.ts

@@ -0,0 +1,3 @@
+export default function calculateNebTm(sequence: any, primerConc: any, { monovalentCationConc }?: {
+    monovalentCationConc: any;
+}): string | number;

package/calculatePercentGC.d.ts

@@ -0,0 +1 @@
+export default function calculatePercentGC(bps: any): number;

package/calculateTm.d.ts

@@ -0,0 +1,2 @@
+declare function _default(sequence: string, type: string, A: Double, R: Double, C: any, Na: Double): Double;
+export default _default;

package/computeDigestFragments.d.ts

@@ -0,0 +1,27 @@
+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 function getDigestFragsForSeqAndEnzymes({ sequence, circular, enzymes, includeOverAndUnderHangs }: {
+    sequence: any;
+    circular: any;
+    enzymes: any;
+    includeOverAndUnderHangs: any;
+}): {
+    computePartialDigestDisabled: any;
+    computeDigestDisabled: any;
+    fragments: any[];
+    overlappingEnzymes: any[];
+};

package/condensePairwiseAlignmentDifferences.d.ts

@@ -0,0 +1 @@
+export default function condensePairwiseAlignmentDifferences(referenceSeq: any, alignedSeq: any): string;

package/convertAACaretPositionOrRangeToDna.d.ts

@@ -0,0 +1 @@
+export default function convertAACaretPositionOrRangeToDna(rangeOrCaret: any): any;

package/convertDnaCaretPositionOrRangeToAA.d.ts

@@ -0,0 +1 @@
+export default function convertDnaCaretPositionOrRangeToAA(rangeOrCaret: any): any;

package/cutSequenceByRestrictionEnzyme.d.ts

@@ -0,0 +1 @@
+export default function cutSequenceByRestrictionEnzyme(pSequence: any, circular: any, restrictionEnzyme: any): any[];

package/defaultEnzymesByName.d.ts

@@ -0,0 +1,2 @@
+export default defaultEnzymesByName;
+declare const defaultEnzymesByName: {};

package/degenerateDnaToAminoAcidMap.d.ts

@@ -0,0 +1,2 @@
+export default degenerateDnaToAminoAcidMap;
+declare const degenerateDnaToAminoAcidMap: import("lodash").Dictionary<string>;

package/degenerateRnaToAminoAcidMap.d.ts

@@ -0,0 +1,2 @@
+export default degenerateRnaToAminoAcidMap;
+declare const degenerateRnaToAminoAcidMap: import("lodash").Dictionary<string>;

package/deleteSequenceDataAtRange.d.ts

@@ -0,0 +1 @@
+export default function deleteSequenceDataAtRange(sequenceData: any, range: any): any;

package/diffUtils.d.ts

@@ -0,0 +1,7 @@
+export function getDiffFromSeqs(oldData: any, newData: any, { ignoreKeys }?: {
+    ignoreKeys?: any[] | undefined;
+}): import("jsondiffpatch").Delta | undefined;
+export function patchSeqWithDiff(oldData: any, diff: any, { ignoreKeys }?: {
+    ignoreKeys?: any[] | undefined;
+}): any;
+export function reverseSeqDiff(diff: any): import("jsondiffpatch").Delta | undefined;

package/doesEnzymeChopOutsideOfRecognitionSite.d.ts

@@ -0,0 +1 @@
+export default function doesEnzymeChopOutsideOfRecognitionSite(enzyme: any): boolean;

package/featureTypesAndColors.d.ts

@@ -0,0 +1,12 @@
+export function getGenbankFeatureToColorMap(): {};
+export const genbankFeatureTypes: {
+    name: string;
+    color: string;
+}[];
+export function getFeatureToColorMap({ includeHidden }?: {
+    includeHidden: any;
+}): {};
+export function getFeatureTypes({ includeHidden }?: {
+    includeHidden: any;
+}): any[];
+export function getMergedFeatureMap(): any;

package/filterAminoAcidSequenceString.d.ts

@@ -0,0 +1 @@
+export default function filterAminoAcidSequenceString(sequenceString: any, options: any): any;

package/filterSequenceString.d.ts

@@ -0,0 +1 @@
+export default function filterSequenceString(sequenceString: any, additionalValidChars: string | undefined, charOverrides: any): any;

package/findNearestRangeOfSequenceOverlapToPosition.d.ts

@@ -0,0 +1,2 @@
+export default findNearestRangeOfSequenceOverlapToPosition;
+declare function findNearestRangeOfSequenceOverlapToPosition(sequenceToSearch: any, overlapSequence: any, positionStart: any, isLinear: any): any;

package/findOrfsInPlasmid.d.ts

@@ -0,0 +1 @@
+export default function findOrfsInPlasmid(sequence: any, circular: any, minimumOrfSize: any, useAdditionalOrfStartCodons: any): Teselagen.bio.orf.ORF[];

package/findSequenceMatches.d.ts

@@ -0,0 +1 @@
+export default function findSequenceMatches(sequence: any, searchString: any, options?: {}): any[];

package/generateAnnotations.d.ts

@@ -0,0 +1,2 @@
+export default generateAnnotations;
+declare function generateAnnotations(numberOfAnnotationsToGenerate: any, start: any, end: any, maxLength: any): {};

package/generateSequenceData.d.ts

@@ -0,0 +1,19 @@
+export default function generateSequenceData({ isProtein, sequenceLength, numFeatures, numParts, numPrimers, numTranslations }?: {
+    isProtein: any;
+    sequenceLength?: number | undefined;
+    numFeatures: any;
+    numParts: any;
+    numPrimers: any;
+    numTranslations: any;
+}): {
+    circular: boolean;
+    name: string;
+    description: string;
+    isProtein: any;
+    sequence: string | false;
+    proteinSequence: any;
+    translations: {} | undefined;
+    features: {};
+    primers: {} | undefined;
+    parts: {};
+};

package/getAllInsertionsInSeqReads.d.ts

@@ -0,0 +1 @@
+export default function getAllInsertionsInSeqReads(seqReads: any): any[];