@teselagen/sequence-utils 0.3.31 → 0.3.32-beta.2

package/findApproxMatches.d.ts

@@ -0,0 +1,10 @@
+/**
+ * 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 default function findApproxMatches(searchSeq: string, targetSeq: string, maxMismatches: number, circular?: boolean): any[];

package/findApproxMatches.test.d.ts

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

package/findOrfsInPlasmid.d.ts

@@ -7,5 +7,5 @@ export default function findOrfsInPlasmid(sequence: any, circular: any, minimumO
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: any;
+    id: string;
 }[];

package/getOrfsFromSequence.d.ts

@@ -16,5 +16,5 @@ export default function getOrfsFromSequence(options: any): {
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: any;
+    id: string;
 }[];

package/index.cjs

@@ -2736,30 +2736,31 @@ function adjustRangeToDeletionOfAnotherRange(rangeToBeAdjusted, anotherRange, ma
     anotherRange,
     maxLength
   );
-  if (trimmedRange) {
-    const nonCircularDeletionRanges = splitRangeIntoTwoPartsIfItIsCircular(
-      anotherRange,
-      maxLength
-    );
-    nonCircularDeletionRanges.forEach(function(nonCircularDeletionRange) {
-      const deletionLength = nonCircularDeletionRange.end - nonCircularDeletionRange.start + 1;
-      if (trimmedRange.start > trimmedRange.end) {
-        if (nonCircularDeletionRange.start < trimmedRange.end) {
-          trimmedRange.start -= deletionLength;
-          trimmedRange.end -= deletionLength;
-        } else if (nonCircularDeletionRange.start < trimmedRange.start) {
-          trimmedRange.start -= deletionLength;
-        } else ;
-      } else {
-        if (nonCircularDeletionRange.start < trimmedRange.start) {
-          trimmedRange.start -= deletionLength;
-          trimmedRange.end -= deletionLength;
-        } else if (nonCircularDeletionRange.start < trimmedRange.end) {
-          trimmedRange.end -= deletionLength;
-        } else ;
-      }
-    });
+  if (!trimmedRange) {
+    return null;
   }
+  const nonCircularDeletionRanges = splitRangeIntoTwoPartsIfItIsCircular(
+    anotherRange,
+    maxLength
+  );
+  nonCircularDeletionRanges.forEach(function(nonCircularDeletionRange) {
+    const deletionLength = nonCircularDeletionRange.end - nonCircularDeletionRange.start + 1;
+    if (trimmedRange.start > trimmedRange.end) {
+      if (nonCircularDeletionRange.start < trimmedRange.end) {
+        trimmedRange.start -= deletionLength;
+        trimmedRange.end -= deletionLength;
+      } else if (nonCircularDeletionRange.start < trimmedRange.start) {
+        trimmedRange.start -= deletionLength;
+      } else ;
+    } else {
+      if (nonCircularDeletionRange.start < trimmedRange.start) {
+        trimmedRange.start -= deletionLength;
+        trimmedRange.end -= deletionLength;
+      } else if (nonCircularDeletionRange.start < trimmedRange.end) {
+        trimmedRange.end -= deletionLength;
+      } else ;
+    }
+  });
   return trimmedRange;
 }
 __name(adjustRangeToDeletionOfAnotherRange, "adjustRangeToDeletionOfAnotherRange");
@@ -3666,307 +3667,15 @@ const getFeatureToColorMap = /* @__PURE__ */ __name(({ includeHidden } = {}) =>
 const getFeatureTypes = /* @__PURE__ */ __name(({ includeHidden } = {}) => filter(getMergedFeatureMap(), (f) => includeHidden ? true : !f.isHidden).map(
   (f) => f.name
 ), "getFeatureTypes");
-function getDefaultExportFromCjs(x) {
-  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
-}
-__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
-var lib = { exports: {} };
-var randomFromSeed;
-var hasRequiredRandomFromSeed;
-function requireRandomFromSeed() {
-  if (hasRequiredRandomFromSeed) return randomFromSeed;
-  hasRequiredRandomFromSeed = 1;
-  var seed = 1;
-  function getNextValue() {
-    seed = (seed * 9301 + 49297) % 233280;
-    return seed / 233280;
-  }
-  __name(getNextValue, "getNextValue");
-  function setSeed(_seed_) {
-    seed = _seed_;
-  }
-  __name(setSeed, "setSeed");
-  randomFromSeed = {
-    nextValue: getNextValue,
-    seed: setSeed
-  };
-  return randomFromSeed;
-}
-__name(requireRandomFromSeed, "requireRandomFromSeed");
-var alphabet_1;
-var hasRequiredAlphabet;
-function requireAlphabet() {
-  if (hasRequiredAlphabet) return alphabet_1;
-  hasRequiredAlphabet = 1;
-  var randomFromSeed2 = requireRandomFromSeed();
-  var ORIGINAL = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_-";
-  var alphabet;
-  var previousSeed;
-  var shuffled;
-  function reset() {
-    shuffled = false;
-  }
-  __name(reset, "reset");
-  function setCharacters(_alphabet_) {
-    if (!_alphabet_) {
-      if (alphabet !== ORIGINAL) {
-        alphabet = ORIGINAL;
-        reset();
-      }
-      return;
-    }
-    if (_alphabet_ === alphabet) {
-      return;
-    }
-    if (_alphabet_.length !== ORIGINAL.length) {
-      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. You submitted " + _alphabet_.length + " characters: " + _alphabet_);
-    }
-    var unique = _alphabet_.split("").filter(function(item, ind, arr) {
-      return ind !== arr.lastIndexOf(item);
-    });
-    if (unique.length) {
-      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. These characters were not unique: " + unique.join(", "));
-    }
-    alphabet = _alphabet_;
-    reset();
-  }
-  __name(setCharacters, "setCharacters");
-  function characters(_alphabet_) {
-    setCharacters(_alphabet_);
-    return alphabet;
-  }
-  __name(characters, "characters");
-  function setSeed(seed) {
-    randomFromSeed2.seed(seed);
-    if (previousSeed !== seed) {
-      reset();
-      previousSeed = seed;
-    }
-  }
-  __name(setSeed, "setSeed");
-  function shuffle() {
-    if (!alphabet) {
-      setCharacters(ORIGINAL);
-    }
-    var sourceArray = alphabet.split("");
-    var targetArray = [];
-    var r = randomFromSeed2.nextValue();
-    var characterIndex;
-    while (sourceArray.length > 0) {
-      r = randomFromSeed2.nextValue();
-      characterIndex = Math.floor(r * sourceArray.length);
-      targetArray.push(sourceArray.splice(characterIndex, 1)[0]);
-    }
-    return targetArray.join("");
-  }
-  __name(shuffle, "shuffle");
-  function getShuffled() {
-    if (shuffled) {
-      return shuffled;
-    }
-    shuffled = shuffle();
-    return shuffled;
-  }
-  __name(getShuffled, "getShuffled");
-  function lookup(index) {
-    var alphabetShuffled = getShuffled();
-    return alphabetShuffled[index];
-  }
-  __name(lookup, "lookup");
-  function get2() {
-    return alphabet || ORIGINAL;
-  }
-  __name(get2, "get");
-  alphabet_1 = {
-    get: get2,
-    characters,
-    seed: setSeed,
-    lookup,
-    shuffled: getShuffled
-  };
-  return alphabet_1;
-}
-__name(requireAlphabet, "requireAlphabet");
-var randomByteBrowser;
-var hasRequiredRandomByteBrowser;
-function requireRandomByteBrowser() {
-  if (hasRequiredRandomByteBrowser) return randomByteBrowser;
-  hasRequiredRandomByteBrowser = 1;
-  var crypto = typeof window === "object" && (window.crypto || window.msCrypto);
-  var randomByte;
-  if (!crypto || !crypto.getRandomValues) {
-    randomByte = /* @__PURE__ */ __name(function(size) {
-      var bytes = [];
-      for (var i = 0; i < size; i++) {
-        bytes.push(Math.floor(Math.random() * 256));
-      }
-      return bytes;
-    }, "randomByte");
-  } else {
-    randomByte = /* @__PURE__ */ __name(function(size) {
-      return crypto.getRandomValues(new Uint8Array(size));
-    }, "randomByte");
-  }
-  randomByteBrowser = randomByte;
-  return randomByteBrowser;
-}
-__name(requireRandomByteBrowser, "requireRandomByteBrowser");
-var format_browser;
-var hasRequiredFormat_browser;
-function requireFormat_browser() {
-  if (hasRequiredFormat_browser) return format_browser;
-  hasRequiredFormat_browser = 1;
-  format_browser = /* @__PURE__ */ __name(function(random, alphabet, size) {
-    var mask = (2 << Math.log(alphabet.length - 1) / Math.LN2) - 1;
-    var step = -~(1.6 * mask * size / alphabet.length);
-    var id = "";
-    while (true) {
-      var bytes = random(step);
-      var i = step;
-      while (i--) {
-        id += alphabet[bytes[i] & mask] || "";
-        if (id.length === +size) return id;
-      }
-    }
-  }, "format_browser");
-  return format_browser;
-}
-__name(requireFormat_browser, "requireFormat_browser");
-var generate_1;
-var hasRequiredGenerate;
-function requireGenerate() {
-  if (hasRequiredGenerate) return generate_1;
-  hasRequiredGenerate = 1;
-  var alphabet = requireAlphabet();
-  var random = requireRandomByteBrowser();
-  var format = /* @__PURE__ */ requireFormat_browser();
-  function generate(number) {
-    var loopCounter = 0;
-    var done;
-    var str = "";
-    while (!done) {
-      str = str + format(random, alphabet.get(), 1);
-      done = number < Math.pow(16, loopCounter + 1);
-      loopCounter++;
-    }
-    return str;
-  }
-  __name(generate, "generate");
-  generate_1 = generate;
-  return generate_1;
-}
-__name(requireGenerate, "requireGenerate");
-var build_1;
-var hasRequiredBuild;
-function requireBuild() {
-  if (hasRequiredBuild) return build_1;
-  hasRequiredBuild = 1;
-  var generate = requireGenerate();
-  requireAlphabet();
-  var REDUCE_TIME = 1567752802062;
-  var version = 7;
-  var counter;
-  var previousSeconds;
-  function build(clusterWorkerId) {
-    var str = "";
-    var seconds = Math.floor((Date.now() - REDUCE_TIME) * 1e-3);
-    if (seconds === previousSeconds) {
-      counter++;
-    } else {
-      counter = 0;
-      previousSeconds = seconds;
-    }
-    str = str + generate(version);
-    str = str + generate(clusterWorkerId);
-    if (counter > 0) {
-      str = str + generate(counter);
-    }
-    str = str + generate(seconds);
-    return str;
-  }
-  __name(build, "build");
-  build_1 = build;
-  return build_1;
-}
-__name(requireBuild, "requireBuild");
-var isValid;
-var hasRequiredIsValid;
-function requireIsValid() {
-  if (hasRequiredIsValid) return isValid;
-  hasRequiredIsValid = 1;
-  var alphabet = requireAlphabet();
-  function isShortId(id) {
-    if (!id || typeof id !== "string" || id.length < 6) {
-      return false;
-    }
-    var nonAlphabetic = new RegExp("[^" + alphabet.get().replace(/[|\\{}()[\]^$+*?.-]/g, "\\$&") + "]");
-    return !nonAlphabetic.test(id);
-  }
-  __name(isShortId, "isShortId");
-  isValid = isShortId;
-  return isValid;
-}
-__name(requireIsValid, "requireIsValid");
-var clusterWorkerIdBrowser;
-var hasRequiredClusterWorkerIdBrowser;
-function requireClusterWorkerIdBrowser() {
-  if (hasRequiredClusterWorkerIdBrowser) return clusterWorkerIdBrowser;
-  hasRequiredClusterWorkerIdBrowser = 1;
-  clusterWorkerIdBrowser = 0;
-  return clusterWorkerIdBrowser;
-}
-__name(requireClusterWorkerIdBrowser, "requireClusterWorkerIdBrowser");
-var hasRequiredLib;
-function requireLib() {
-  if (hasRequiredLib) return lib.exports;
-  hasRequiredLib = 1;
-  (function(module2) {
-    var alphabet = requireAlphabet();
-    var build = requireBuild();
-    var isValid2 = requireIsValid();
-    var clusterWorkerId = requireClusterWorkerIdBrowser() || 0;
-    function seed(seedValue) {
-      alphabet.seed(seedValue);
-      return module2.exports;
-    }
-    __name(seed, "seed");
-    function worker(workerId) {
-      clusterWorkerId = workerId;
-      return module2.exports;
-    }
-    __name(worker, "worker");
-    function characters(newCharacters) {
-      if (newCharacters !== void 0) {
-        alphabet.characters(newCharacters);
-      }
-      return alphabet.shuffled();
-    }
-    __name(characters, "characters");
-    function generate() {
-      return build(clusterWorkerId);
-    }
-    __name(generate, "generate");
-    module2.exports = generate;
-    module2.exports.generate = generate;
-    module2.exports.seed = seed;
-    module2.exports.worker = worker;
-    module2.exports.characters = characters;
-    module2.exports.isValid = isValid2;
-  })(lib);
-  return lib.exports;
-}
-__name(requireLib, "requireLib");
-var shortid$1;
-var hasRequiredShortid;
-function requireShortid() {
-  if (hasRequiredShortid) return shortid$1;
-  hasRequiredShortid = 1;
-  shortid$1 = requireLib();
-  return shortid$1;
-}
-__name(requireShortid, "requireShortid");
-var shortidExports = requireShortid();
-const shortid = /* @__PURE__ */ getDefaultExportFromCjs(shortidExports);
+const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
+let nanoid = /* @__PURE__ */ __name((size = 21) => {
+  let id = "";
+  let bytes = crypto.getRandomValues(new Uint8Array(size |= 0));
+  while (size--) {
+    id += urlAlphabet[bytes[size] & 63];
+  }
+  return id;
+}, "nanoid");
 function cutSequenceByRestrictionEnzyme(pSequence, circular, restrictionEnzyme) {
   if (restrictionEnzyme.forwardRegex.length === 0 || restrictionEnzyme.reverseRegex.length === 0) {
     const returnArray = [];
@@ -4174,7 +3883,7 @@ function cutSequence(forwardRegExpPattern, restrictionEnzyme, sequence, circular
       }
       const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
       restrictionCutSite = {
-        id: shortid(),
+        id: nanoid(),
         start,
         end,
         topSnipPosition,
@@ -4232,7 +3941,7 @@ function computeDigestFragments({
   });
   if (!circular && cutsites.length) {
     sortedCutsites.push({
-      id: "seqTerm_" + shortid(),
+      id: "seqTerm_" + nanoid(),
       start: 0,
       end: 0,
       overhangBps: "",
@@ -4366,6 +4075,10 @@ function getDigestFragsForSeqAndEnzymes({
   });
 }
 __name(getDigestFragsForSeqAndEnzymes, "getDigestFragsForSeqAndEnzymes");
+function getDefaultExportFromCjs(x) {
+  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
+}
+__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
 var jsondiffpatch_umd$1 = { exports: {} };
 var empty = {};
 var hasRequiredEmpty;
@@ -8964,10 +8677,10 @@ function tidyUpAnnotation(_annotation, {
     annotation.name = "Untitled annotation";
   }
   if (provideNewIdsForAnnotations) {
-    annotation.id = shortid();
+    annotation.id = nanoid();
   }
   if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-    annotation.id = shortid();
+    annotation.id = nanoid();
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id
     );
@@ -9211,7 +8924,7 @@ function tidyUpSequenceData(pSeqData, options = {}) {
         if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
-          itemId = shortid();
+          itemId = nanoid();
           if (!doNotProvideIdsForAnnotations) {
             item.id = itemId;
           }
@@ -9514,6 +9227,36 @@ function insertGapsIntoRefSeq(refSeq, seqReads) {
   return refSeqWithGaps.join("");
 }
 __name(insertGapsIntoRefSeq, "insertGapsIntoRefSeq");
+function findApproxMatches(searchSeq, targetSeq, maxMismatches, circular = false) {
+  const matches = [];
+  const lenA = searchSeq.length;
+  const lenB = targetSeq.length;
+  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 window2 = targetSeqExtended.slice(i, i + lenA);
+    let mismatchCount = 0;
+    const mismatchPositions = [];
+    for (let j = 0; j < lenA; j++) {
+      if (searchSeq[j] !== window2[j]) {
+        mismatchPositions.push(j);
+        mismatchCount++;
+        if (mismatchCount > maxMismatches) break;
+      }
+    }
+    if (mismatchCount <= maxMismatches) {
+      matches.push({
+        index: i,
+        match: window2,
+        mismatchPositions,
+        numMismatches: mismatchPositions.length
+        // Keep for backwards compatibility
+      });
+    }
+  }
+  return matches;
+}
+__name(findApproxMatches, "findApproxMatches");
 var spliceString$1;
 var hasRequiredSpliceString;
 function requireSpliceString() {
@@ -17751,7 +17494,7 @@ function generateAnnotation(start, end, maxLength) {
   return __spreadProps(__spreadValues({}, range), {
     name: getRandomInt(0, 1e5).toString(),
     type: "misc_feature",
-    id: shortid(),
+    id: nanoid(),
     forward: Math.random() > 0.5,
     notes: {}
   });
@@ -17874,7 +17617,7 @@ function getOrfsFromSequence(options) {
           forward,
           annotationTypePlural: "orfs",
           isOrf: true,
-          id: shortid()
+          id: nanoid()
         });
       }
     }
@@ -19322,6 +19065,7 @@ exports.doesEnzymeChopOutsideOfRecognitionSite = doesEnzymeChopOutsideOfRecognit
 exports.featureColors = featureColors;
 exports.filterRnaString = filterRnaString;
 exports.filterSequenceString = filterSequenceString;
+exports.findApproxMatches = findApproxMatches;
 exports.findNearestRangeOfSequenceOverlapToPosition = findNearestRangeOfSequenceOverlapToPosition;
 exports.findOrfsInPlasmid = findOrfsInPlasmid;
 exports.findSequenceMatches = findSequenceMatches;

package/index.d.ts

@@ -11,6 +11,7 @@ export { default as getDegenerateRnaStringFromAAString } from './getDegenerateRn
 export { default as getVirtualDigest } from './getVirtualDigest';
 export { default as isEnzymeType2S } from './isEnzymeType2S';
 export { default as insertGapsIntoRefSeq } from './insertGapsIntoRefSeq';
+export { default as findApproxMatches } from './findApproxMatches';
 export { default as adjustBpsToReplaceOrInsert } from './adjustBpsToReplaceOrInsert';
 export { default as calculatePercentGC } from './calculatePercentGC';
 export { default as calculateTm } from './calculateTm';