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

package/src/proteinAlphabet.ts

@@ -1,271 +0,0 @@
-const proteinAlphabet = {
-  A: {
-    value: "A",
-    name: "Alanine",
-    threeLettersName: "Ala",
-    hydrophobicity: 1.8,
-    colorByFamily: "#00FFFF",
-    color: "hsl(327.3, 100%, 69%)",
-    mass: 71.0779
-  },
-  R: {
-    value: "R",
-    name: "Arginine",
-    threeLettersName: "Arg",
-    hydrophobicity: -4.5,
-    colorByFamily: "#FFC0CB",
-    color: "hsl(258.1, 100%, 69%)",
-    mass: 156.18568
-  },
-
-  N: {
-    value: "N",
-    name: "Asparagine",
-    threeLettersName: "Asn",
-    hydrophobicity: -3.5,
-    colorByFamily: "#D3D3D3",
-    color: "hsl(268.9, 100%, 69%)",
-    mass: 114.10264
-  },
-  D: {
-    value: "D",
-    name: "Aspartic acid",
-    threeLettersName: "Asp",
-    hydrophobicity: -3.5,
-    colorByFamily: "#EE82EE",
-    color: "hsl(268.9, 100%, 69%)",
-    mass: 115.0874
-  },
-  C: {
-    value: "C",
-    name: "Cysteine",
-    threeLettersName: "Cys",
-    hydrophobicity: 2.5,
-    colorByFamily: "#FFFF00",
-    color: "hsl(335.1, 100%, 69%)",
-    mass: 103.1429
-  },
-
-  E: {
-    value: "E",
-    name: "Glutamic acid",
-    threeLettersName: "Glu",
-    hydrophobicity: -3.5,
-    colorByFamily: "#EE82EE",
-    color: "hsl(268.9, 100%, 69%)",
-    mass: 129.11398
-  },
-  Q: {
-    value: "Q",
-    name: "Glutamine",
-    threeLettersName: "Gln",
-    hydrophobicity: -3.5,
-    colorByFamily: "#D3D3D3",
-    color: "hsl(268.9, 100%, 69%)",
-    mass: 128.12922
-  },
-  G: {
-    value: "G",
-    name: "Glycine",
-    threeLettersName: "Gly",
-    hydrophobicity: -0.4,
-    colorByFamily: "#00FFFF",
-    color: "hsl(303.1, 100%, 69%)",
-    mass: 57.05132
-  },
-
-  H: {
-    value: "H",
-    name: "Histidine",
-    threeLettersName: "His",
-    hydrophobicity: -3.2,
-    colorByFamily: "#FFC0CB",
-    color: "hsl(272.2, 100%, 69%)",
-    mass: 137.13928
-  },
-
-  I: {
-    value: "I",
-    name: "Isoleucine ",
-    threeLettersName: "Ile",
-    hydrophobicity: 4.5,
-    colorByFamily: "#00FFFF",
-    color: "hsl(356.9, 100%, 69%)",
-    mass: 113.15764
-  },
-  L: {
-    value: "L",
-    name: "Leucine",
-    threeLettersName: "Leu",
-    hydrophobicity: 3.8,
-    colorByFamily: "#00FFFF",
-    color: "hsl(349.4, 100%, 69%)",
-    mass: 113.15764
-  },
-  K: {
-    value: "K",
-    name: "Lysine",
-    threeLettersName: "Lys",
-    hydrophobicity: -3.9,
-    colorByFamily: "#FFC0CB",
-    color: "hsl(264.7, 100%, 69%)",
-    mass: 128.17228
-  },
-
-  O: {
-    value: "O",
-    name: "Pyrrolysine",
-    threeLettersName: "Pyl",
-    colorByFamily: "#FFC0CB",
-    color: "hsl(264.7, 100%, 69%)",
-    mass: 255.313
-  },
-
-  M: {
-    value: "M",
-    name: "Methionine",
-    threeLettersName: "Met",
-    hydrophobicity: 1.9,
-    colorByFamily: "#FFFF00",
-    color: "hsl(328.5, 100%, 69%)",
-    mass: 131.19606
-  },
-  F: {
-    value: "F",
-    name: "Phenylalanine",
-    threeLettersName: "Phe",
-    hydrophobicity: 2.8,
-    colorByFamily: "#FFA500",
-    color: "hsl(338.4, 100%, 69%)",
-    mass: 147.17386
-  },
-  P: {
-    value: "P",
-    name: "Proline",
-    threeLettersName: "Pro",
-    hydrophobicity: -1.6,
-    colorByFamily: "#00FFFF",
-    color: "hsl(289.9, 100%, 69%)",
-    mass: 97.11518
-  },
-  S: {
-    value: "S",
-    name: "Serine",
-    threeLettersName: "Ser",
-    hydrophobicity: -0.8,
-    colorByFamily: "#90EE90",
-    color: "hsl(298.6, 100%, 69%)",
-    mass: 87.0773
-  },
-  T: {
-    value: "T",
-    name: "Threonine",
-    threeLettersName: "Thr",
-    hydrophobicity: -0.7,
-    colorByFamily: "#90EE90",
-    color: "hsl(299.8, 100%, 69%)",
-    mass: 101.10388
-  },
-  U: {
-    value: "U",
-    name: "Selenocysteine",
-    threeLettersName: "Sec",
-    colorByFamily: "#FF0000",
-    color: "hsl(0, 100%, 69%)",
-    mass: 150.3079
-  },
-  W: {
-    value: "W",
-    name: "Tryptophan",
-    threeLettersName: "Trp",
-    hydrophobicity: -0.9,
-    colorByFamily: "#FFA500",
-    color: "hsl(297.6, 100%, 69%)",
-    mass: 186.2099
-  },
-  Y: {
-    value: "Y",
-    name: "Tyrosine",
-    threeLettersName: "Tyr",
-    hydrophobicity: -1.3,
-    colorByFamily: "#FFA500",
-    color: "hsl(293.2, 100%, 69%)",
-    mass: 163.17326
-  },
-  V: {
-    value: "V",
-    name: "Valine",
-    threeLettersName: "Val",
-    hydrophobicity: 4.2,
-    colorByFamily: "#00FFFF",
-    color: "hsl(353.6, 100%, 69%)",
-    mass: 99.13106
-  },
-  "*": {
-    value: "*",
-    name: "Stop",
-    threeLettersName: "Stop",
-    colorByFamily: "#FF0000",
-    color: "hsl(0, 100%, 69%)",
-    mass: 0
-  },
-  ".": {
-    //tnr: this is actually a deletion/gap character (previously we had this as a stop character which is incorrect) https://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html
-    value: ".",
-    name: "Gap",
-    threeLettersName: "Gap",
-    colorByFamily: "#FF0000",
-    color: "hsl(0, 100%, 69%)",
-    mass: 0
-  },
-  "-": {
-    value: "-",
-    name: "Gap",
-    threeLettersName: "Gap",
-    colorByFamily: "#FF0000",
-    color: "hsl(0, 100%, 69%)",
-    mass: 0
-  },
-  B: {
-    value: "B",
-    threeLettersName: "ND",
-    colorByFamily: "#D3D3D3",
-    color: "hsl(268.9, 100%, 69%)",
-    isAmbiguous: true,
-    name: "B",
-    aliases: "ND",
-    mass: 0
-  },
-  J: {
-    value: "J",
-    threeLettersName: "IL",
-    colorByFamily: "#00FFFF",
-    color: "hsl(352, 100%, 69%)",
-    isAmbiguous: true,
-    name: "J",
-    aliases: "IL",
-    mass: 0
-  },
-  X: {
-    value: "X",
-    threeLettersName: "ACDEFGHIKLMNPQRSTVWY",
-    colorByFamily: "#FFFFFF",
-    color: "hsl(60, 100%, 69%)",
-    isAmbiguous: true,
-    name: "X",
-    aliases: "ACDEFGHIKLMNPQRSTVWY",
-    mass: 0
-  },
-  Z: {
-    value: "Z",
-    threeLettersName: "QE",
-    colorByFamily: "#D3D3D3",
-    color: "hsl(268.9, 100%, 69%)",
-    isAmbiguous: true,
-    name: "Z",
-    aliases: "QE",
-    mass: 0
-  }
-};
-
-export default proteinAlphabet;

package/src/rotateBpsToPosition.ts

@@ -1,12 +0,0 @@
-export default function rotateBpsToPosition(
-  bps: string,
-  caretPosition: number
-) {
-  return arrayRotate(bps.split(""), caretPosition).join("");
-}
-
-function arrayRotate<T>(arr: T[], count: number): T[] {
-  count -= arr.length * Math.floor(count / arr.length);
-  arr.push(...arr.splice(0, count));
-  return arr;
-}

package/src/rotateSequenceDataToPosition.ts

@@ -1,54 +0,0 @@
-import { map } from "lodash-es";
-import { adjustRangeToRotation } from "@teselagen/range-utils";
-import tidyUpSequenceData, {
-  TidyUpSequenceDataOptions
-} from "./tidyUpSequenceData";
-import { modifiableTypes } from "./annotationTypes";
-import rotateBpsToPosition from "./rotateBpsToPosition";
-import { SequenceData, Annotation } from "./types";
-
-export default function rotateSequenceDataToPosition(
-  sequenceData: SequenceData,
-  caretPosition: number,
-  options: TidyUpSequenceDataOptions = {}
-) {
-  const newSequenceData = tidyUpSequenceData(sequenceData, {
-    doNotRemoveInvalidChars: true,
-    ...options
-  });
-
-  //update the sequence
-  newSequenceData.sequence = rotateBpsToPosition(
-    newSequenceData.sequence,
-    caretPosition
-  );
-
-  //handle the insert
-  modifiableTypes.forEach(annotationType => {
-    //update the annotations:
-    //handle the delete if necessary
-    newSequenceData[annotationType] = adjustAnnotationsToRotation(
-      newSequenceData[annotationType] as Annotation[],
-      caretPosition,
-      newSequenceData.sequence.length
-    );
-  });
-  return newSequenceData;
-}
-
-function adjustAnnotationsToRotation(
-  annotationsToBeAdjusted: Annotation[],
-  positionToRotateTo: number,
-  maxLength: number
-) {
-  return map(annotationsToBeAdjusted, annotation => {
-    return {
-      ...adjustRangeToRotation(annotation, positionToRotateTo, maxLength),
-      locations: annotation.locations
-        ? annotation.locations.map(location =>
-            adjustRangeToRotation(location, positionToRotateTo, maxLength)
-          )
-        : undefined
-    };
-  }).filter(range => !!range); //filter any fully deleted ranges
-}

package/src/shiftAnnotationsByLen.ts

@@ -1,24 +0,0 @@
-import { modifiableTypes } from "./annotationTypes";
-import adjustAnnotationsToInsert from "./adjustAnnotationsToInsert";
-import { SequenceData } from "./types";
-
-export default function shiftAnnotationsByLen({
-  seqData,
-  caretPosition,
-  insertLength
-}: {
-  seqData: SequenceData;
-  caretPosition: number;
-  insertLength: number;
-}) {
-  modifiableTypes.forEach(annotationType => {
-    const existingAnnotations = seqData[annotationType];
-    if (existingAnnotations) {
-      seqData[annotationType] = adjustAnnotationsToInsert(
-        existingAnnotations,
-        caretPosition,
-        insertLength
-      );
-    }
-  });
-}

package/src/threeLetterSequenceStringToAminoAcidMap.ts

@@ -1,198 +0,0 @@
-import proteinAlphabet from "./proteinAlphabet";
-
-const initThreeLetterSequenceStringToAminoAcidMap: Record<
-  string,
-  {
-    value: string;
-    name: string;
-    threeLettersName: string;
-    hydrophobicity?: number;
-    colorByFamily: string;
-    color: string;
-    mass: number;
-    isAmbiguous?: boolean;
-    aliases?: string;
-  }
-> = {
-  gct: proteinAlphabet.A,
-  gcc: proteinAlphabet.A,
-  gca: proteinAlphabet.A,
-  gcg: proteinAlphabet.A,
-  gcu: proteinAlphabet.A,
-  cgt: proteinAlphabet.R,
-  cgc: proteinAlphabet.R,
-  cga: proteinAlphabet.R,
-  cgg: proteinAlphabet.R,
-  aga: proteinAlphabet.R,
-  agg: proteinAlphabet.R,
-  cgu: proteinAlphabet.R,
-  aat: proteinAlphabet.N,
-  aac: proteinAlphabet.N,
-  aau: proteinAlphabet.N,
-  gat: proteinAlphabet.D,
-  gac: proteinAlphabet.D,
-  gau: proteinAlphabet.D,
-  tgt: proteinAlphabet.C,
-  tgc: proteinAlphabet.C,
-  ugu: proteinAlphabet.C,
-  ugc: proteinAlphabet.C,
-  gaa: proteinAlphabet.E,
-  gag: proteinAlphabet.E,
-  caa: proteinAlphabet.Q,
-  cag: proteinAlphabet.Q,
-  ggt: proteinAlphabet.G,
-  ggc: proteinAlphabet.G,
-  gga: proteinAlphabet.G,
-  ggg: proteinAlphabet.G,
-  ggu: proteinAlphabet.G,
-  cat: proteinAlphabet.H,
-  cac: proteinAlphabet.H,
-  cau: proteinAlphabet.H,
-  att: proteinAlphabet.I,
-  atc: proteinAlphabet.I,
-  ata: proteinAlphabet.I,
-  auu: proteinAlphabet.I,
-  auc: proteinAlphabet.I,
-  aua: proteinAlphabet.I,
-  ctt: proteinAlphabet.L,
-  ctc: proteinAlphabet.L,
-  cta: proteinAlphabet.L,
-  ctg: proteinAlphabet.L,
-  tta: proteinAlphabet.L,
-  ttg: proteinAlphabet.L,
-  cuu: proteinAlphabet.L,
-  cuc: proteinAlphabet.L,
-  cua: proteinAlphabet.L,
-  cug: proteinAlphabet.L,
-  uua: proteinAlphabet.L,
-  uug: proteinAlphabet.L,
-  aaa: proteinAlphabet.K,
-  aag: proteinAlphabet.K,
-  atg: proteinAlphabet.M,
-  aug: proteinAlphabet.M,
-  ttt: proteinAlphabet.F,
-  ttc: proteinAlphabet.F,
-  uuu: proteinAlphabet.F,
-  uuc: proteinAlphabet.F,
-  cct: proteinAlphabet.P,
-  ccc: proteinAlphabet.P,
-  cca: proteinAlphabet.P,
-  ccg: proteinAlphabet.P,
-  ccu: proteinAlphabet.P,
-  tct: proteinAlphabet.S,
-  tcc: proteinAlphabet.S,
-  tca: proteinAlphabet.S,
-  tcg: proteinAlphabet.S,
-  agt: proteinAlphabet.S,
-  agc: proteinAlphabet.S,
-  ucu: proteinAlphabet.S,
-  ucc: proteinAlphabet.S,
-  uca: proteinAlphabet.S,
-  ucg: proteinAlphabet.S,
-  agu: proteinAlphabet.S,
-  act: proteinAlphabet.T,
-  acc: proteinAlphabet.T,
-  aca: proteinAlphabet.T,
-  acg: proteinAlphabet.T,
-  acu: proteinAlphabet.T,
-  tgg: proteinAlphabet.W,
-  ugg: proteinAlphabet.W,
-  tat: proteinAlphabet.Y,
-  tac: proteinAlphabet.Y,
-  uau: proteinAlphabet.Y,
-  uac: proteinAlphabet.Y,
-  gtt: proteinAlphabet.V,
-  gtc: proteinAlphabet.V,
-  gta: proteinAlphabet.V,
-  gtg: proteinAlphabet.V,
-  guu: proteinAlphabet.V,
-  guc: proteinAlphabet.V,
-  gua: proteinAlphabet.V,
-  gug: proteinAlphabet.V,
-  taa: proteinAlphabet["*"],
-  tag: proteinAlphabet["*"],
-  tga: proteinAlphabet["*"],
-  uaa: proteinAlphabet["*"],
-  uag: proteinAlphabet["*"],
-  uga: proteinAlphabet["*"],
-  "...": proteinAlphabet["."],
-  "---": proteinAlphabet["-"]
-};
-
-// IUPAC nucleotide codes (DNA/RNA) with U awareness
-const IUPAC: Record<string, string[]> = {
-  A: ["A"],
-  C: ["C"],
-  G: ["G"],
-  T: ["T"],
-  U: ["U"],
-
-  R: ["A", "G"],
-  Y: ["C", "T", "U"],
-  K: ["G", "T", "U"],
-  M: ["A", "C"],
-  S: ["G", "C"],
-  W: ["A", "T", "U"],
-  B: ["C", "G", "T", "U"],
-  D: ["A", "G", "T", "U"],
-  H: ["A", "C", "T", "U"],
-  V: ["A", "C", "G"],
-  N: ["A", "C", "G", "T", "U"],
-  X: ["A", "C", "G", "T", "U"]
-};
-
-function expandAndResolve(threeLetterCodon: string) {
-  const chars = threeLetterCodon.toUpperCase().split("");
-  const picks = chars.map(c => IUPAC[c] || [c]);
-
-  let allPossibleThreeLetterCodons = [""];
-  for (const set of picks) {
-    const next = [];
-    for (const prefix of allPossibleThreeLetterCodons)
-      for (const b of set) next.push(prefix + b);
-    allPossibleThreeLetterCodons = next;
-  }
-  let foundAminoAcid = null;
-  for (const codon of allPossibleThreeLetterCodons) {
-    const lowerCodon = codon.toLowerCase();
-    const aminoAcidObj =
-      initThreeLetterSequenceStringToAminoAcidMap[lowerCodon] ??
-      initThreeLetterSequenceStringToAminoAcidMap[
-        lowerCodon.replace(/u/g, "t")
-      ] ??
-      initThreeLetterSequenceStringToAminoAcidMap[
-        lowerCodon.replace(/t/g, "u")
-      ];
-    if (aminoAcidObj) {
-      if (!foundAminoAcid) {
-        foundAminoAcid = aminoAcidObj;
-      } else if (foundAminoAcid.value !== aminoAcidObj.value) {
-        return null;
-      }
-    } else {
-      return null;
-    }
-  }
-  return foundAminoAcid;
-}
-
-function getCodonToAminoAcidMap() {
-  const map = initThreeLetterSequenceStringToAminoAcidMap;
-  // generate all IUPAC 3-mers
-  const codes = Object.keys(IUPAC);
-  for (const a of codes)
-    for (const b of codes)
-      for (const c of codes) {
-        const codon = a + b + c;
-        const lowerCodon = codon.toLowerCase();
-        if (map[lowerCodon]) continue;
-        const aminoAcidObj = expandAndResolve(codon);
-        if (aminoAcidObj) map[lowerCodon] = aminoAcidObj;
-      }
-
-  return map;
-}
-
-const threeLetterSequenceStringToAminoAcidMap = getCodonToAminoAcidMap();
-
-export default threeLetterSequenceStringToAminoAcidMap;