@teselagen/sequence-utils 0.3.38-beta.3 → 0.3.41

package/src/diffUtils.ts

@@ -1,80 +0,0 @@
-import { cloneDeep, forEach } from "lodash-es";
-import { diff, patch, reverse, Delta } from "jsondiffpatch";
-import { SequenceData } from "./types";
-
-import tidyUpSequenceData from "./tidyUpSequenceData";
-
-interface DiffOptions {
-  ignoreKeys?: string[];
-}
-
-const getDiffFromSeqs = (
-  oldData: SequenceData,
-  newData: SequenceData,
-  { ignoreKeys = [] }: DiffOptions = {}
-): Delta | undefined => {
-  /* eslint-disable-next-line @typescript-eslint/no-explicit-any */
-  const cleanedOldData: any = tidyUpSequenceData(oldData, {
-    annotationsAsObjects: true,
-    noTranslationData: true,
-    doNotRemoveInvalidChars: true
-  });
-  /* eslint-disable-next-line @typescript-eslint/no-explicit-any */
-  const cleanedNewData: any = tidyUpSequenceData(newData, {
-    annotationsAsObjects: true,
-    noTranslationData: true,
-    doNotRemoveInvalidChars: true
-  });
-
-  [cleanedOldData, cleanedNewData].forEach(d => {
-    [
-      "cutsites",
-      "orfs",
-      "filteredFeatures",
-      "size",
-      "fromFileUpload",
-      "description",
-      "materiallyAvailable",
-      ...ignoreKeys
-    ].forEach(prop => {
-      delete d[prop];
-    });
-    if (d.translations) {
-      forEach(d.translations, (translation, key) => {
-        if (
-          translation.translationType &&
-          translation.translationType !== "User Created"
-        ) {
-          delete d.translations[key];
-        } else {
-          delete translation.aminoAcids;
-        }
-      });
-    }
-  });
-
-  return diff(cleanedOldData, cleanedNewData);
-};
-
-const patchSeqWithDiff = (
-  oldData: SequenceData,
-  diffData: Delta,
-  { ignoreKeys = [] }: DiffOptions = {}
-): SequenceData => {
-  ignoreKeys.forEach(k => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    delete (diffData as any)[k];
-  });
-  const tidyOld = tidyUpSequenceData(cloneDeep(oldData), {
-    annotationsAsObjects: true,
-    doNotRemoveInvalidChars: true
-  });
-
-  return patch(tidyOld, diffData) as SequenceData;
-};
-
-const reverseSeqDiff = (diffData: Delta): Delta | undefined => {
-  return reverse(diffData);
-};
-
-export { getDiffFromSeqs, patchSeqWithDiff, reverseSeqDiff };

package/src/doesEnzymeChopOutsideOfRecognitionSite.ts

@@ -1,16 +0,0 @@
-import { RestrictionEnzyme } from "./types";
-
-export default function doesEnzymeChopOutsideOfRecognitionSite(
-  enzyme: RestrictionEnzyme
-): boolean {
-  if (
-    enzyme.topSnipOffset &&
-    enzyme.bottomSnipOffset &&
-    (enzyme.topSnipOffset > enzyme.site.length ||
-      enzyme.bottomSnipOffset > enzyme.site.length)
-  ) {
-    return true;
-  } else {
-    return false;
-  }
-}

package/src/featureTypesAndColors.ts

@@ -1,167 +0,0 @@
-import { get, keyBy, filter } from "lodash-es";
-
-interface FeatureType {
-  name: string;
-  color: string;
-  isHidden?: boolean;
-  isGenbankStandardType?: boolean;
-  isOverridden?: boolean;
-  isCustomType?: boolean;
-}
-
-const genbankFeatureTypes: FeatureType[] = [
-  { name: "-10_signal", color: "#4ECDC4" },
-  { name: "-35_signal", color: "#F7FFF7" },
-  { name: "3'clip", color: "#FF6B6B" },
-  { name: "3'UTR", color: "#FFE66D" },
-  { name: "5'clip", color: "#3E517A" },
-  { name: "5'UTR", color: "#BBBBBB" },
-  { name: "D-loop", color: "#F13C73" },
-  { name: "assembly_gap", color: "#DE9151" },
-  { name: "centromere", color: "#F34213" },
-  { name: "Het", color: "#BC5D2E" },
-  { name: "mobile_element", color: "#6DB1BF" },
-  { name: "ncRNA", color: "#FFEAEC" },
-  { name: "proprotein", color: "#F39A9D" },
-  { name: "regulatory", color: "#3F6C51" },
-  { name: "SecStr", color: "#7B4B94" },
-  { name: "Site", color: "#7D82B8" },
-  { name: "telomere", color: "#DE9151" },
-  { name: "tmRNA", color: "#B7E3CC" },
-  { name: "unsure", color: "#C4FFB2" },
-  { name: "V_segment", color: "#D6F7A3" },
-  { name: "allele", color: "#D86D6D" },
-  { name: "attenuator", color: "#6B7F9C" },
-  { name: "C_region", color: "#B5D89D" },
-  { name: "CAAT_signal", color: "#E9CD98" },
-  { name: "CDS", color: "#EF6500" },
-  { name: "conserved", color: "#A3A5F0" },
-  { name: "D_segment", color: "#C060F7" },
-  { name: "default", color: "#CCCCCC" },
-  { name: "enhancer", color: "#38F872" },
-  { name: "exon", color: "#95F844" },
-  { name: "gap", color: "#F7D43C" },
-  { name: "GC_signal", color: "#861F1F" },
-  { name: "gene", color: "#684E27" },
-  { name: "iDNA", color: "#A59B41" },
-  { name: "intron", color: "#52963E" },
-  { name: "J_region", color: "#369283" },
-  { name: "LTR", color: "#31748F" },
-  { name: "m_rna", color: "#FFFF00" },
-  { name: "mat_peptide", color: "#353E8F" },
-  { name: "misc_binding", color: "#006FEF" },
-  { name: "misc_difference", color: "#5A368A" },
-  { name: "misc_feature", color: "#006FEF" },
-  { name: "misc_marker", color: "#8DCEB1" },
-  { name: "misc_part", color: "#006FEF" },
-  { name: "misc_recomb", color: "#DD97B4" },
-  { name: "misc_RNA", color: "#BD0101" },
-  { name: "misc_signal", color: "#FF9A04" },
-  { name: "misc_structure", color: "#B3FF00" },
-  { name: "modified_base", color: "#00F7FF" },
-  { name: "mRNA", color: "#FFD900" },
-  { name: "N_region", color: "#AE00FF" },
-  { name: "old_sequence", color: "#F0A7FF" },
-  { name: "operator", color: "#63004D" },
-  { name: "operon", color: "#000653" },
-  { name: "oriT", color: "#580000" },
-  { name: "plasmid", color: "#00635E" },
-  { name: "polyA_signal", color: "#BBBBBB" },
-  { name: "polyA_site", color: "#003328" },
-  { name: "precursor_RNA", color: "#443200" },
-  { name: "prim_transcript", color: "#665E4C" },
-  { name: "primer_bind", color: "#53d969" },
-  { name: "promoter", color: "#31B440" },
-  { name: "protein_bind", color: "#2E2E2E" },
-  { name: "protein_domain", color: "#4D4B4B" },
-  { name: "protein", color: "#696969" },
-  { name: "RBS", color: "#BDFFCB" },
-  { name: "rep_origin", color: "#878787" },
-  { name: "repeat_region", color: "#966363" },
-  { name: "repeat_unit", color: "#A16D8D" },
-  { name: "rRNA", color: "#9BF0FF" },
-  { name: "s_mutation", color: "#70A2FF" },
-  { name: "S_region", color: "#FF74A9" },
-  { name: "satellite", color: "#164E64" },
-  { name: "scRNA", color: "#A057FF" },
-  { name: "sig_peptide", color: "#2FFF8D" },
-  { name: "snoRNA", color: "#296B14" },
-  { name: "snRNA", color: "#A16249" },
-  { name: "source", color: "#0B17BD" },
-  { name: "start", color: "#D6A336" },
-  { name: "stem_loop", color: "#67069E" },
-  { name: "stop", color: "#D44FC9" },
-  { name: "STS", color: "#597FE7" },
-  { name: "tag", color: "#E419DA" },
-  { name: "TATA_signal", color: "#EB2B2B" },
-  { name: "terminator", color: "#F51600" },
-  { name: "transit_peptide", color: "#24D491" },
-  { name: "transposon", color: "#B6E436" },
-  { name: "tRNA", color: "#D1456F" },
-  { name: "V_region", color: "#7B5EE7" },
-  { name: "variation", color: "#2EE455" }
-];
-
-const getMergedFeatureMap = (): Record<string, FeatureType> => {
-  const keyedGBFeats = keyBy(
-    genbankFeatureTypes.map(f => ({
-      ...f,
-      isGenbankStandardType: true
-    })),
-    "name"
-  );
-  const featureOverrides: FeatureType[] =
-    ((typeof window !== "undefined" &&
-      get(window, "tg_featureTypeOverrides")) as unknown as FeatureType[]) ||
-    ((typeof global !== "undefined" &&
-      get(global, "tg_featureTypeOverrides")) as unknown as FeatureType[]) ||
-    [];
-
-  const mappedOverrides = featureOverrides.map(fo => {
-    const originalGenbankFeat = keyedGBFeats[fo.name];
-    return {
-      ...originalGenbankFeat,
-      ...fo,
-      ...(originalGenbankFeat ? { isOverridden: true } : { isCustomType: true })
-    };
-  });
-  const keyedOverrides = keyBy(mappedOverrides, "name");
-
-  return {
-    ...keyedGBFeats,
-    ...keyedOverrides
-  };
-};
-
-const getFeatureToColorMap = ({
-  includeHidden
-}: { includeHidden?: boolean } = {}): Record<string, string> => {
-  const toRet: Record<string, string> = {};
-  filter(getMergedFeatureMap(), f =>
-    includeHidden ? true : !f.isHidden
-  ).forEach(f => {
-    toRet[f.name] = f.color;
-  });
-  return toRet;
-};
-
-const getFeatureTypes = ({
-  includeHidden
-}: { includeHidden?: boolean } = {}): string[] =>
-  filter(getMergedFeatureMap(), f => (includeHidden ? true : !f.isHidden)).map(
-    f => f.name
-  );
-
-export { genbankFeatureTypes };
-
-export function getGenbankFeatureToColorMap(): Record<string, string> {
-  const toRet: Record<string, string> = {};
-  genbankFeatureTypes.forEach(({ name, color }) => {
-    toRet[name] = color;
-  });
-  return toRet;
-}
-
-export { getFeatureToColorMap };
-export { getFeatureTypes };
-export { getMergedFeatureMap };

package/src/filterSequenceString.ts

@@ -1,153 +0,0 @@
-import { debounce, uniq } from "lodash-es";
-import {
-  ambiguous_dna_letters,
-  ambiguous_rna_letters,
-  extended_protein_letters
-} from "./bioData";
-
-let allWarnings: string[] = [];
-
-let makeToast = () => {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  if (typeof window !== "undefined" && (window as any).toastr && allWarnings.length) {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    (window as any).toastr.warning(uniq(allWarnings).join("\n"));
-  }
-  allWarnings = [];
-};
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-(makeToast as any) = debounce(makeToast, 200);
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function showWarnings(warnings: any) {
-  allWarnings = allWarnings.concat(warnings);
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  (makeToast as any).cancel();
-  makeToast();
-}
-
-interface FilterSequenceStringOptions {
-  additionalValidChars?: string;
-  isOligo?: boolean;
-  name?: string;
-  isProtein?: boolean;
-  isRna?: boolean;
-  isMixedRnaAndDna?: boolean;
-  [key: string]: unknown;
-}
-
-export default function filterSequenceString(
-  sequenceString = "",
-  {
-    additionalValidChars = "",
-    isOligo,
-    name,
-    isProtein,
-    isRna,
-    isMixedRnaAndDna
-  }: FilterSequenceStringOptions = {}
-): [string, string[]] {
-  const acceptedChars = getAcceptedChars({
-    isOligo,
-    isProtein,
-    isRna,
-    isMixedRnaAndDna
-  });
-  const replaceChars = getReplaceChars({
-    isOligo,
-    isProtein,
-    isRna,
-    isMixedRnaAndDna
-  });
-
-  let sanitizedVal = "";
-  const invalidChars: string[] = [];
-  const chars = `${acceptedChars}${additionalValidChars.split("").join("\\")}`;
-  const warnings: string[] = [];
-  const replaceCount: Record<string, number> = {};
-  sequenceString.split("").forEach(letter => {
-    const lowerLetter = letter.toLowerCase();
-    if (replaceChars && replaceChars[lowerLetter]) {
-      if (!replaceCount[lowerLetter]) {
-        replaceCount[lowerLetter] = 0;
-      }
-      replaceCount[lowerLetter]++;
-      const isUpper = lowerLetter !== letter;
-      sanitizedVal += isUpper
-        ? replaceChars[lowerLetter].toUpperCase()
-        : replaceChars[lowerLetter];
-    } else if (chars.includes(lowerLetter)) {
-      sanitizedVal += letter;
-    } else {
-      invalidChars.push(letter);
-    }
-  });
-  //add replace count warnings
-  Object.keys(replaceCount).forEach(letter => {
-    warnings.push(
-      `Replaced "${letter}" with "${replaceChars[letter]}"${replaceCount[letter] > 1 ? ` ${replaceCount[letter]} times` : ""
-      }`
-    );
-  });
-  if (sequenceString.length !== sanitizedVal.length) {
-    warnings.push(
-      `${name ? `Sequence ${name}: ` : ""
-      }Invalid character(s) detected and removed: ${uniq(invalidChars)
-        .map(c => {
-          if (c === " ") {
-            return "space";
-          }
-          return c;
-        })
-        .slice(0, 100)
-        .join(", ")} `
-    );
-  }
-  showWarnings(warnings);
-
-  return [sanitizedVal, warnings];
-}
-
-export function getAcceptedChars({
-  isOligo,
-  isProtein,
-  isRna,
-  isMixedRnaAndDna
-}: FilterSequenceStringOptions = {}) {
-  return isProtein
-    ? `${extended_protein_letters.toLowerCase()}`
-    : isOligo
-      ? ambiguous_rna_letters.toLowerCase() + "t"
-      : isRna
-        ? ambiguous_rna_letters.toLowerCase() + "t"
-        : isMixedRnaAndDna
-          ? ambiguous_rna_letters.toLowerCase() +
-          ambiguous_dna_letters.toLowerCase()
-          : //just plain old dna
-          ambiguous_rna_letters.toLowerCase() +
-          ambiguous_dna_letters.toLowerCase();
-}
-export function getReplaceChars({
-  isOligo,
-  isProtein,
-  isRna,
-  isMixedRnaAndDna
-}: FilterSequenceStringOptions = {}): Record<string, string> {
-  return isProtein
-    ? {}
-    : // {".": "*"}
-    isOligo
-      ? {}
-      : isRna
-        ? { t: "u" }
-        : isMixedRnaAndDna
-          ? {}
-          : //just plain old dna
-          {};
-}
-
-export const filterRnaString = (
-  s: string,
-  o: FilterSequenceStringOptions
-): string => filterSequenceString(s, { ...o, isRna: true })[0];

package/src/findApproxMatches.ts

@@ -1,58 +0,0 @@
-/**
- * Find approximate matches of a search sequence within a target sequence
- *
- * @param {string} searchSeq - The sequence to search for
- * @param {string} targetSeq - The sequence to search within
- * @param {number} maxMismatches - Maximum number of mismatches allowed
- * @param {boolean} circular - Whether to treat the target sequence as circular (default: false)
- * @returns {Array} - Array of objects containing { index, match, mismatchPositions }
- */
-
-export interface ApproxMatch {
-  index: number;
-  match: string;
-  mismatchPositions: number[];
-  numMismatches: number;
-}
-
-export default function findApproxMatches(
-  searchSeq: string,
-  targetSeq: string,
-  maxMismatches: number,
-  circular = false
-): ApproxMatch[] {
-  const matches: ApproxMatch[] = [];
-  const lenA = searchSeq.length;
-  const lenB = targetSeq.length;
-
-  // Extend targetSeq to simulate circularity, in case circular = true
-  const targetSeqExtended = circular
-    ? targetSeq + targetSeq.slice(0, lenA - 1)
-    : targetSeq;
-  const limit = circular ? lenB : lenB - lenA + 1;
-
-  for (let i = 0; i < limit; i++) {
-    const window = targetSeqExtended.slice(i, i + lenA);
-    let mismatchCount = 0;
-    const mismatchPositions: number[] = [];
-
-    for (let j = 0; j < lenA; j++) {
-      if (searchSeq[j] !== window[j]) {
-        mismatchPositions.push(j);
-        mismatchCount++;
-        if (mismatchCount > maxMismatches) break;
-      }
-    }
-
-    if (mismatchCount <= maxMismatches) {
-      matches.push({
-        index: i,
-        match: window,
-        mismatchPositions,
-        numMismatches: mismatchPositions.length // Keep for backwards compatibility
-      });
-    }
-  }
-
-  return matches;
-}

package/src/findNearestRangeOfSequenceOverlapToPosition.ts

@@ -1,43 +0,0 @@
-import { normalizeRange, Range } from "@teselagen/range-utils";
-function findNearestRangeOfSequenceOverlapToPosition(
-  sequenceToSearch: string,
-  overlapSequence: string,
-  positionStart = 0,
-  isLinear?: boolean
-): Range | null {
-  if (sequenceToSearch.length < overlapSequence.length) {
-    return null;
-  }
-  const regex = new RegExp(overlapSequence, "ig");
-  let result: RegExpExecArray | null;
-  let index: number | undefined;
-  let distance = Infinity;
-  while (
-    (result = regex.exec(sequenceToSearch + (isLinear ? "" : sequenceToSearch)))
-  ) {
-    if (result.index > sequenceToSearch.length) break;
-    let newDistance = Math.abs(result.index - positionStart);
-    newDistance = isLinear
-      ? newDistance //if linear, don't check around the origin
-      : Math.min(newDistance, Math.abs(newDistance - sequenceToSearch.length));
-    if (newDistance > distance) {
-      break;
-    }
-    index = result.index;
-    distance = newDistance;
-  }
-
-  if (index === undefined) {
-    return null;
-  }
-
-  //index is the closest range start
-  return normalizeRange(
-    {
-      start: index,
-      end: index + overlapSequence.length - 1
-    },
-    sequenceToSearch.length
-  );
-}
-export default findNearestRangeOfSequenceOverlapToPosition;

package/src/findOrfsInPlasmid.ts

@@ -1,31 +0,0 @@
-import getOrfsFromSequence, { Orf } from "./getOrfsFromSequence";
-
-export default function findOrfsInPlasmid(
-  sequence: string,
-  circular: boolean,
-  minimumOrfSize: number,
-  useAdditionalOrfStartCodons: boolean,
-  isProteinOrOligo: boolean
-): Orf[] {
-  if (isProteinOrOligo) {
-    // we do not find ORFs in protein/oligo sequences
-    return [];
-  }
-  //tnr, we should do the parsing down of the orfs immediately after they're returned from this sequence
-  // const orfs1Forward = eliminateCircularOrfsThatOverlapWithNonCircularOrfs(getOrfsFromSequence(0, doubleForwardSequence, minimumOrfSize, true), maxLength);
-  const forwardOrfs = getOrfsFromSequence({
-    sequence: sequence,
-    minimumOrfSize: minimumOrfSize,
-    forward: true,
-    circular: circular,
-    useAdditionalOrfStartCodons
-  });
-  const reverseOrfs = getOrfsFromSequence({
-    sequence: sequence,
-    minimumOrfSize: minimumOrfSize,
-    forward: false,
-    circular: circular,
-    useAdditionalOrfStartCodons
-  });
-  return forwardOrfs.concat(reverseOrfs);
-}