@teselagen/sequence-utils 0.3.6 → 0.3.8

package/README.md

@@ -0,0 +1,89 @@
+<!-- TOC -->
+
+- [[CHANGELOG](CHANGELOG.md)](#changelogchangelogmd)
+- [Installing](#installing)
+- [Usage](#usage)
+- [About this Repo](#about-this-repo)
+- [Editing This Repo:](#editing-this-repo)
+  - [All collaborators:](#all-collaborators)
+- [Updating this repo:](#updating-this-repo)
+  - [Teselagen collaborators:](#teselagen-collaborators)
+  - [Outside collaborators:](#outside-collaborators)
+- [Building](#building)
+- [Running unit tests](#running-unit-tests)
+
+<!-- /TOC -->
+
+## [CHANGELOG](CHANGELOG.md)
+
+## Installing
+
+```
+npm install @teselagen/sequence-utils
+```
+
+## Usage
+
+```
+import { getComplementSequence } from '@teselagen/sequence-utils';
+
+const mySequence = 'ATGAGAG';
+const myComplement = getComplementSequence(mySequence);
+console.log(myComplement); // TACTCTC
+```
+
+## About this Repo
+
+This is a collection of dna sequence utility functions.
+
+All sequences and annotations (unless otherwise specified) are assumed to have 0-based inclusive indices.
+
+```
+  Example:
+  0123456
+  ATGAGAG
+  --fff--  (the feature covers GAG)
+  0-based inclusive start:
+  feature.start = 2
+  1-based inclusive start:
+  feature.start = 3
+  0-based inclusive end:
+  feature.end = 4
+  1-based inclusive end:
+  feature.end = 5
+```
+
+## Editing This Repo:
+
+### All collaborators:
+
+Edit/create a new file and update/add any relevant tests.
+Make sure they pass by running `npm test`
+
+## Updating this repo:
+
+Commit and push all changes first (make sure tests are passing!)
+
+### Teselagen collaborators:
+
+Commit and push all changes
+Sign into npm using the teselagen npm account (npm whoami)
+
+```
+npm version patch|minor|major
+npm publish
+```
+
+### Outside collaborators:
+
+fork and pull request please :)
+
+This library was generated with [Nx](https://nx.dev).
+
+## Building
+
+Run `nx build sequence-utils` to build the library.
+
+## Running unit tests
+
+Run `nx test sequence-utils` to execute the unit tests via [Jest](https://jestjs.io).

package/bioData.d.ts

@@ -1,29 +1,5 @@
 export const protein_letters: "ACDEFGHIKLMNPQRSTVWY";
 export const extended_protein_letters: "ACDEFGHIKLMNPQRSTVWYBXZJUO.*-";
-export namespace protein_letters_1to3 {
-    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";
 export const ambiguous_rna_letters: "GAUCRYWSMKHBVDN";
@@ -48,195 +24,6 @@ export const ambiguous_dna_values: {
     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 {
-    let A_1: number;
-    export { A_1 as A };
-    let C_1: number;
-    export { C_1 as C };
-    let G_1: number;
-    export { G_1 as G };
-    let T_1: number;
-    export { T_1 as T };
-}
-export namespace monoisotopic_unambiguous_dna_weights {
-    let A_2: number;
-    export { A_2 as A };
-    let C_2: number;
-    export { C_2 as C };
-    let G_2: number;
-    export { G_2 as G };
-    let T_2: number;
-    export { T_2 as T };
-}
-export namespace unambiguous_rna_weights {
-    let A_3: number;
-    export { A_3 as A };
-    let C_3: number;
-    export { C_3 as C };
-    let G_3: number;
-    export { G_3 as G };
-    let U_1: number;
-    export { U_1 as U };
-}
-export namespace monoisotopic_unambiguous_rna_weights {
-    let A_4: number;
-    export { A_4 as A };
-    let C_4: number;
-    export { C_4 as C };
-    let G_4: number;
-    export { G_4 as G };
-    let U_2: number;
-    export { U_2 as U };
-}
-export namespace protein_weights {
-    let A_5: number;
-    export { A_5 as A };
-    let C_5: number;
-    export { C_5 as C };
-    let D_1: number;
-    export { D_1 as D };
-    let E_1: number;
-    export { E_1 as E };
-    let F_1: number;
-    export { F_1 as F };
-    let G_5: number;
-    export { G_5 as G };
-    let H_1: number;
-    export { H_1 as H };
-    let I_1: number;
-    export { I_1 as I };
-    let K_1: number;
-    export { K_1 as K };
-    let L_1: number;
-    export { L_1 as L };
-    let M_1: number;
-    export { M_1 as M };
-    let N_1: number;
-    export { N_1 as N };
-    let O_1: number;
-    export { O_1 as O };
-    let P_1: number;
-    export { P_1 as P };
-    let Q_1: number;
-    export { Q_1 as Q };
-    let R_1: number;
-    export { R_1 as R };
-    let S_1: number;
-    export { S_1 as S };
-    let T_3: number;
-    export { T_3 as T };
-    let U_3: number;
-    export { U_3 as U };
-    let V_1: number;
-    export { V_1 as V };
-    let W_1: number;
-    export { W_1 as W };
-    let Y_1: number;
-    export { Y_1 as Y };
-}
-export namespace monoisotopic_protein_weights {
-    let A_6: number;
-    export { A_6 as A };
-    let C_6: number;
-    export { C_6 as C };
-    let D_2: number;
-    export { D_2 as D };
-    let E_2: number;
-    export { E_2 as E };
-    let F_2: number;
-    export { F_2 as F };
-    let G_6: number;
-    export { G_6 as G };
-    let H_2: number;
-    export { H_2 as H };
-    let I_2: number;
-    export { I_2 as I };
-    let K_2: number;
-    export { K_2 as K };
-    let L_2: number;
-    export { L_2 as L };
-    let M_2: number;
-    export { M_2 as M };
-    let N_2: number;
-    export { N_2 as N };
-    let O_2: number;
-    export { O_2 as O };
-    let P_2: number;
-    export { P_2 as P };
-    let Q_2: number;
-    export { Q_2 as Q };
-    let R_2: number;
-    export { R_2 as R };
-    let S_2: number;
-    export { S_2 as S };
-    let T_4: number;
-    export { T_4 as T };
-    let U_4: number;
-    export { U_4 as U };
-    let V_2: number;
-    export { V_2 as V };
-    let W_2: number;
-    export { W_2 as W };
-    let Y_2: number;
-    export { Y_2 as Y };
-}
 export const extended_protein_values: {
     A: string;
     B: string;
@@ -268,129 +55,3 @@ export const extended_protein_values: {
     ".": string;
     "-": string;
 };
-export namespace atom_weights {
-    let H_3: number;
-    export { H_3 as H };
-    let D_3: number;
-    export { D_3 as D };
-    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 };
-    let N_3: number;
-    export { N_3 as N };
-    let O_3: number;
-    export { O_3 as O };
-    let F_3: number;
-    export { F_3 as F };
-    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 };
-    let S_3: number;
-    export { S_3 as S };
-    export let Cl: number;
-    export let Ar: number;
-    let K_3: number;
-    export { K_3 as K };
-    export let Ca: number;
-    export let Sc: number;
-    export let Ti: number;
-    let V_3: number;
-    export { V_3 as V };
-    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 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 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 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 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/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 };