@teselagen/sequence-utils 0.1.12 → 0.1.14

package/addGapsToSeqReads.test.d.ts

@@ -0,0 +1 @@
+export {};

package/adjustBpsToReplaceOrInsert.test.d.ts

@@ -0,0 +1 @@
+export {};

package/aminoAcidToDnaRna.test.d.ts

@@ -0,0 +1 @@
+export {};

package/annotateSingleSeq.test.d.ts

@@ -0,0 +1 @@
+export {};

package/autoAnnotate.test.d.ts

@@ -0,0 +1 @@
+export {};

package/bioData.d.ts

@@ -1,28 +1,28 @@
 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;
+    let A: string;
+    let C: string;
+    let D: string;
+    let E: string;
+    let F: string;
+    let G: string;
+    let H: string;
+    let I: string;
+    let K: string;
+    let L: string;
+    let M: string;
+    let N: string;
+    let P: string;
+    let Q: string;
+    let R: string;
+    let S: string;
+    let T: string;
+    let V: string;
+    let W: string;
+    let Y: string;
+    let O: string;
+    let U: string;
 }
 export const ambiguous_dna_letters: "GATCRYWSMKHBVDN";
 export const unambiguous_dna_letters: "GATC";
@@ -106,135 +106,135 @@ export const ambiguous_rna_complement: {
     N: string;
 };
 export namespace unambiguous_dna_weights {
-    const A_1: number;
+    let A_1: number;
     export { A_1 as A };
-    const C_1: number;
+    let C_1: number;
     export { C_1 as C };
-    const G_1: number;
+    let G_1: number;
     export { G_1 as G };
-    const T_1: number;
+    let T_1: number;
     export { T_1 as T };
 }
 export namespace monoisotopic_unambiguous_dna_weights {
-    const A_2: number;
+    let A_2: number;
     export { A_2 as A };
-    const C_2: number;
+    let C_2: number;
     export { C_2 as C };
-    const G_2: number;
+    let G_2: number;
     export { G_2 as G };
-    const T_2: number;
+    let T_2: number;
     export { T_2 as T };
 }
 export namespace unambiguous_rna_weights {
-    const A_3: number;
+    let A_3: number;
     export { A_3 as A };
-    const C_3: number;
+    let C_3: number;
     export { C_3 as C };
-    const G_3: number;
+    let G_3: number;
     export { G_3 as G };
-    const U_1: number;
+    let U_1: number;
     export { U_1 as U };
 }
 export namespace monoisotopic_unambiguous_rna_weights {
-    const A_4: number;
+    let A_4: number;
     export { A_4 as A };
-    const C_4: number;
+    let C_4: number;
     export { C_4 as C };
-    const G_4: number;
+    let G_4: number;
     export { G_4 as G };
-    const U_2: number;
+    let U_2: number;
     export { U_2 as U };
 }
 export namespace protein_weights {
-    const A_5: number;
+    let A_5: number;
     export { A_5 as A };
-    const C_5: number;
+    let C_5: number;
     export { C_5 as C };
-    const D_1: number;
+    let D_1: number;
     export { D_1 as D };
-    const E_1: number;
+    let E_1: number;
     export { E_1 as E };
-    const F_1: number;
+    let F_1: number;
     export { F_1 as F };
-    const G_5: number;
+    let G_5: number;
     export { G_5 as G };
-    const H_1: number;
+    let H_1: number;
     export { H_1 as H };
-    const I_1: number;
+    let I_1: number;
     export { I_1 as I };
-    const K_1: number;
+    let K_1: number;
     export { K_1 as K };
-    const L_1: number;
+    let L_1: number;
     export { L_1 as L };
-    const M_1: number;
+    let M_1: number;
     export { M_1 as M };
-    const N_1: number;
+    let N_1: number;
     export { N_1 as N };
-    const O_1: number;
+    let O_1: number;
     export { O_1 as O };
-    const P_1: number;
+    let P_1: number;
     export { P_1 as P };
-    const Q_1: number;
+    let Q_1: number;
     export { Q_1 as Q };
-    const R_1: number;
+    let R_1: number;
     export { R_1 as R };
-    const S_1: number;
+    let S_1: number;
     export { S_1 as S };
-    const T_3: number;
+    let T_3: number;
     export { T_3 as T };
-    const U_3: number;
+    let U_3: number;
     export { U_3 as U };
-    const V_1: number;
+    let V_1: number;
     export { V_1 as V };
-    const W_1: number;
+    let W_1: number;
     export { W_1 as W };
-    const Y_1: number;
+    let Y_1: number;
     export { Y_1 as Y };
 }
 export namespace monoisotopic_protein_weights {
-    const A_6: number;
+    let A_6: number;
     export { A_6 as A };
-    const C_6: number;
+    let C_6: number;
     export { C_6 as C };
-    const D_2: number;
+    let D_2: number;
     export { D_2 as D };
-    const E_2: number;
+    let E_2: number;
     export { E_2 as E };
-    const F_2: number;
+    let F_2: number;
     export { F_2 as F };
-    const G_6: number;
+    let G_6: number;
     export { G_6 as G };
-    const H_2: number;
+    let H_2: number;
     export { H_2 as H };
-    const I_2: number;
+    let I_2: number;
     export { I_2 as I };
-    const K_2: number;
+    let K_2: number;
     export { K_2 as K };
-    const L_2: number;
+    let L_2: number;
     export { L_2 as L };
-    const M_2: number;
+    let M_2: number;
     export { M_2 as M };
-    const N_2: number;
+    let N_2: number;
     export { N_2 as N };
-    const O_2: number;
+    let O_2: number;
     export { O_2 as O };
-    const P_2: number;
+    let P_2: number;
     export { P_2 as P };
-    const Q_2: number;
+    let Q_2: number;
     export { Q_2 as Q };
-    const R_2: number;
+    let R_2: number;
     export { R_2 as R };
-    const S_2: number;
+    let S_2: number;
     export { S_2 as S };
-    const T_4: number;
+    let T_4: number;
     export { T_4 as T };
-    const U_4: number;
+    let U_4: number;
     export { U_4 as U };
-    const V_2: number;
+    let V_2: number;
     export { V_2 as V };
-    const W_2: number;
+    let W_2: number;
     export { W_2 as W };
-    const Y_2: number;
+    let Y_2: number;
     export { Y_2 as Y };
 }
 export const extended_protein_values: {
@@ -269,128 +269,128 @@ export const extended_protein_values: {
     "-": string;
 };
 export namespace atom_weights {
-    const H_3: number;
+    let H_3: number;
     export { H_3 as H };
-    const D_3: number;
+    let 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 let He: number;
+    export let Li: number;
+    export let Be: number;
+    export let B: number;
+    let C_7: number;
     export { C_7 as C };
-    const N_3: number;
+    let N_3: number;
     export { N_3 as N };
-    const O_3: number;
+    let O_3: number;
     export { O_3 as O };
-    const F_3: number;
+    let 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 let Ne: number;
+    export let Na: number;
+    export let Mg: number;
+    export let Al: number;
+    export let Si: number;
+    let P_3: number;
     export { P_3 as P };
-    const S_3: number;
+    let S_3: number;
     export { S_3 as S };
-    export const Cl: number;
-    export const Ar: number;
-    const K_3: number;
+    export let Cl: number;
+    export let Ar: number;
+    let 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 let Ca: number;
+    export let Sc: number;
+    export let Ti: number;
+    let 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 let Cr: number;
+    export let Mn: number;
+    export let Fe: number;
+    export let Co: number;
+    export let Ni: number;
+    export let Cu: number;
+    export let Zn: number;
+    export let Ga: number;
+    export let Ge: number;
+    export let As: number;
+    export let Se: number;
+    export let Br: number;
+    export let Kr: number;
+    export let Rb: number;
+    export let Sr: number;
+    let 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 let Zr: number;
+    export let Nb: number;
+    export let Mo: number;
+    export let Tc: number;
+    export let Ru: number;
+    export let Rh: number;
+    export let Pd: number;
+    export let Ag: number;
+    export let Cd: number;
+    export let In: number;
+    export let Sn: number;
+    export let Sb: number;
+    export let Te: number;
+    let 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 let Xe: number;
+    export let Cs: number;
+    export let Ba: number;
+    export let La: number;
+    export let Ce: number;
+    export let Pr: number;
+    export let Nd: number;
+    export let Pm: number;
+    export let Sm: number;
+    export let Eu: number;
+    export let Gd: number;
+    export let Tb: number;
+    export let Dy: number;
+    export let Ho: number;
+    export let Er: number;
+    export let Tm: number;
+    export let Yb: number;
+    export let Lu: number;
+    export let Hf: number;
+    export let Ta: number;
+    let 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 let Re: number;
+    export let Os: number;
+    export let Ir: number;
+    export let Pt: number;
+    export let Au: number;
+    export let Hg: number;
+    export let Tl: number;
+    export let Pb: number;
+    export let Bi: number;
+    export let Po: number;
+    export let At: number;
+    export let Rn: number;
+    export let Fr: number;
+    export let Ra: number;
+    export let Ac: number;
+    export let Th: number;
+    export let Pa: number;
+    let 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;
+    export let Np: number;
+    export let Pu: number;
+    export let Am: number;
+    export let Cm: number;
+    export let Bk: number;
+    export let Cf: number;
+    export let Es: number;
+    export let Fm: number;
+    export let Md: number;
+    export let No: number;
+    export let Lr: number;
+    export let Rf: number;
+    export let Db: number;
+    export let Sg: number;
+    export let Bh: number;
+    export let Hs: number;
+    export let Mt: number;
 }

package/calculateNebTa.test.d.ts

@@ -0,0 +1 @@
+export {};

package/calculateNebTm.test.d.ts

@@ -0,0 +1 @@
+export {};

package/calculatePercentGC.test.d.ts

@@ -0,0 +1 @@
+export {};

package/calculateTm.test.d.ts

@@ -0,0 +1 @@
+export {};

package/computeDigestFragments.test.d.ts

@@ -0,0 +1 @@
+export {};

package/condensePairwiseAlignmentDifferences.test.d.ts

@@ -0,0 +1 @@
+export {};

package/convertAACaretPositionOrRangeToDna.test.d.ts

@@ -0,0 +1 @@
+export {};

package/convertDnaCaretPositionOrRangeToAA.test.d.ts

@@ -0,0 +1 @@
+export {};

package/cutSequenceByRestrictionEnzyme.test.d.ts

@@ -0,0 +1 @@
+export {};

package/deleteSequenceDataAtRange.test.d.ts

@@ -0,0 +1 @@
+export {};

package/diffUtils.test.d.ts

@@ -0,0 +1 @@
+export {};

package/doesEnzymeChopOutsideOfRecognitionSite.test.d.ts

@@ -0,0 +1 @@
+export {};

package/featureTypesAndColors.test.d.ts

@@ -0,0 +1 @@
+export {};

package/filterAminoAcidSequenceString.test.d.ts

@@ -0,0 +1 @@
+export {};

package/filterSequenceString.test.d.ts

@@ -0,0 +1 @@
+export {};

package/findNearestRangeOfSequenceOverlapToPosition.test.d.ts

@@ -0,0 +1 @@
+export {};

package/findSequenceMatches.test.d.ts

@@ -0,0 +1 @@
+export {};

package/generateSequenceData.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getAllInsertionsInSeqReads.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getAminoAcidDataForEachBaseOfDna.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getAminoAcidStringFromSequenceString.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getDigestFragmentsForRestrictionEnzymes.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getInsertBetweenVals.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getLeftAndRightOfSequenceInRangeGivenPosition.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getMassofAaString.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getOrfsFromSequence.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getOverlapBetweenTwoSequences.d.ts

@@ -6,4 +6,4 @@
  * @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, options: object): object;
+export default function getOverlapBetweenTwoSequences(sequenceToFind: string, sequenceToSearchIn: string): object;

package/getOverlapBetweenTwoSequences.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getPossiblePartsFromSequenceAndEnzymes.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getReverseAminoAcidStringFromSequenceString.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getReverseComplementAnnotation.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getReverseComplementSequenceAndAnnotations.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getReverseComplementSequenceString.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getReverseSequenceString.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getSequenceDataBetweenRange.test.d.ts

@@ -0,0 +1 @@
+export {};

package/getVirtualDigest.test.d.ts

@@ -0,0 +1 @@
+export {};

package/guessIfSequenceIsDnaAndNotProtein.test.d.ts

@@ -0,0 +1 @@
+export {};

package/index.d.ts

@@ -73,13 +73,13 @@ export { default as degenerateRnaToAminoAcidMap } from "./degenerateRnaToAminoAc
 export { default as getMassOfAaString } from "./getMassOfAaString";
 export { default as shiftAnnotationsByLen } from "./shiftAnnotationsByLen";
 export { default as adjustAnnotationsToInsert } from "./adjustAnnotationsToInsert";
-import { getFeatureToColorMap } from "./featureTypesAndColors";
-import { getFeatureTypes } from "./featureTypesAndColors";
-import { genbankFeatureTypes } from "./featureTypesAndColors";
-import { getMergedFeatureMap } from "./featureTypesAndColors";
+import { getFeatureToColorMap } from './featureTypesAndColors';
+import { getFeatureTypes } from './featureTypesAndColors';
+import { genbankFeatureTypes } from './featureTypesAndColors';
+import { getMergedFeatureMap } from './featureTypesAndColors';
 export const FeatureTypes: any[];
 export const featureColors: {};
-import { autoAnnotate } from "./autoAnnotate";
-import { convertApELikeRegexToRegex } from "./autoAnnotate";
-import { convertProteinSeqToDNAIupac } from "./autoAnnotate";
+import { autoAnnotate } from './autoAnnotate';
+import { convertApELikeRegexToRegex } from './autoAnnotate';
+import { convertProteinSeqToDNAIupac } from './autoAnnotate';
 export { getFeatureToColorMap, getFeatureTypes, genbankFeatureTypes, getMergedFeatureMap, autoAnnotate, convertApELikeRegexToRegex, convertProteinSeqToDNAIupac };