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

package/index.umd.cjs

@@ -2738,30 +2738,31 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       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");
@@ -3668,307 +3669,15 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   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 = [];
@@ -4176,7 +3885,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
         }
         const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
         restrictionCutSite = {
-          id: shortid(),
+          id: nanoid(),
           start,
           end,
           topSnipPosition,
@@ -4234,7 +3943,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     });
     if (!circular && cutsites.length) {
       sortedCutsites.push({
-        id: "seqTerm_" + shortid(),
+        id: "seqTerm_" + nanoid(),
         start: 0,
         end: 0,
         overhangBps: "",
@@ -4368,6 +4077,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     });
   }
   __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;
@@ -8966,10 +8679,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       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
       );
@@ -9213,7 +8926,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
           if (item.id || item.id === 0) {
             itemId = item.id;
           } else {
-            itemId = shortid();
+            itemId = nanoid();
             if (!doNotProvideIdsForAnnotations) {
               item.id = itemId;
             }
@@ -9516,6 +9229,36 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     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() {
@@ -17753,7 +17496,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     return __spreadProps(__spreadValues({}, range), {
       name: getRandomInt(0, 1e5).toString(),
       type: "misc_feature",
-      id: shortid(),
+      id: nanoid(),
       forward: Math.random() > 0.5,
       notes: {}
     });
@@ -17876,7 +17619,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
             forward,
             annotationTypePlural: "orfs",
             isOrf: true,
-            id: shortid()
+            id: nanoid()
           });
         }
       }
@@ -19324,6 +19067,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   exports2.featureColors = featureColors;
   exports2.filterRnaString = filterRnaString;
   exports2.filterSequenceString = filterSequenceString;
+  exports2.findApproxMatches = findApproxMatches;
   exports2.findNearestRangeOfSequenceOverlapToPosition = findNearestRangeOfSequenceOverlapToPosition;
   exports2.findOrfsInPlasmid = findOrfsInPlasmid;
   exports2.findSequenceMatches = findSequenceMatches;

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.31",
+  "version": "0.3.32-beta.2",
   "type": "module",
   "dependencies": {
+    "@teselagen/range-utils": "0.3.14-beta.1",
     "escape-string-regexp": "5.0.0",
     "jsondiffpatch": "0.4.1",
-    "string-splice": "^1.3.0",
     "lodash-es": "^4.17.21",
-    "shortid": "2.2.16",
-    "@teselagen/range-utils": "0.3.13"
+    "nanoid": "^5.1.5",
+    "string-splice": "^1.3.0"
   },
   "exports": {
     ".": {
@@ -16,5 +16,9 @@
       "require": "./index.cjs"
     }
   },
+  "volta": {
+    "node": "18.18.0",
+    "yarn": "1.22.22"
+  },
   "license": "MIT"
 }

package/src/computeDigestFragments.js

@@ -1,4 +1,4 @@
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 import { flatMap, cloneDeep } from "lodash-es";
 import {
   normalizePositionByRangeLength,
@@ -27,7 +27,7 @@ function computeDigestFragments({
   });
   if (!circular && cutsites.length) {
     sortedCutsites.push({
-      id: "seqTerm_" + shortid(),
+      id: "seqTerm_" + nanoid(),
       start: 0,
       end: 0,
       overhangBps: "",

package/src/cutSequenceByRestrictionEnzyme.js

@@ -1,5 +1,5 @@
 import { assign } from "lodash-es";
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 
 import {
@@ -268,7 +268,7 @@ function cutSequence(
       const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
 
       restrictionCutSite = {
-        id: shortid(),
+        id: nanoid(),
         start,
         end,
         topSnipPosition,

package/src/findApproxMatches.js

@@ -0,0 +1,50 @@
+/**
+ * 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,
+  targetSeq,
+  maxMismatches,
+  circular = false
+) {
+  const matches = [];
+  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 = [];
+
+    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;
+}