@teselagen/bio-parsers 0.4.9 → 0.4.11

package/genbankToJson.d.ts

@@ -1,3 +1,3 @@
-export function parseFeatureLocation(locStr: any, isProtein: any, inclusive1BasedStart: any, inclusive1BasedEnd: any): any[];
+export function parseFeatureLocation(locStr: any, isProtein: any, inclusive1BasedStart: any, inclusive1BasedEnd: any, isCircular: any, sequenceLength: any): any[];
 export default genbankToJson;
 declare function genbankToJson(string: any, options?: {}): any;

package/index.js

@@ -993,7 +993,7 @@ lodash.exports;
         return new LodashWrapper(value);
       }
       __name(lodash2, "lodash");
-      var baseCreate = function() {
+      var baseCreate = /* @__PURE__ */ function() {
         function object() {
         }
         __name(object, "object");
@@ -4618,7 +4618,7 @@ lodash.exports;
       var gte = createRelationalOperation(function(value, other) {
         return value >= other;
       });
-      var isArguments = baseIsArguments(function() {
+      var isArguments = baseIsArguments(/* @__PURE__ */ function() {
         return arguments;
       }()) ? baseIsArguments : function(value) {
         return isObjectLike(value) && hasOwnProperty2.call(value, "callee") && !propertyIsEnumerable.call(value, "callee");
@@ -6169,7 +6169,7 @@ lodash.exports;
   }).call(commonjsGlobal);
 })(lodash, lodash.exports);
 var lodashExports = lodash.exports;
-const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
+const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
 const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
 const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
 const aminoAcidToDegenerateDnaMap = {
@@ -6884,7 +6884,7 @@ __name(requireEmpty, "requireEmpty");
         throw new TypeError("Cannot call a class as a function");
       }
     }, "classCallCheck");
-    var createClass = function() {
+    var createClass = /* @__PURE__ */ function() {
       function defineProperties(target, props) {
         for (var i = 0; i < props.length; i++) {
           var descriptor = props[i];
@@ -6946,7 +6946,7 @@ __name(requireEmpty, "requireEmpty");
       }
       return call && (typeof call === "object" || typeof call === "function") ? call : self2;
     }, "possibleConstructorReturn");
-    var slicedToArray = function() {
+    var slicedToArray = /* @__PURE__ */ function() {
       function sliceIterator(arr, i) {
         var _arr = [];
         var _n = true;
@@ -11274,6 +11274,20 @@ const annotationTypes = [
   "primers",
   "guides"
 ];
+let allWarnings = [];
+let makeToast = /* @__PURE__ */ __name(() => {
+  if (typeof window !== "undefined" && window.toastr && allWarnings.length) {
+    window.toastr.warning(lodashExports.uniq(allWarnings).join("\n"));
+  }
+  allWarnings = [];
+}, "makeToast");
+makeToast = lodashExports.debounce(makeToast, 200);
+function showWarnings(warnings) {
+  allWarnings = allWarnings.concat(warnings);
+  makeToast.cancel();
+  makeToast();
+}
+__name(showWarnings, "showWarnings");
 function filterSequenceString(sequenceString = "", {
   additionalValidChars = "",
   isOligo,
@@ -11321,14 +11335,15 @@ function filterSequenceString(sequenceString = "", {
   });
   if (sequenceString.length !== sanitizedVal.length) {
     warnings.push(
-      `${name ? `Sequence ${name}: ` : ""}Invalid character(s) detected and removed: ${invalidChars.slice(0, 100).join(", ")} `
+      `${name ? `Sequence ${name}: ` : ""}Invalid character(s) detected and removed: ${lodashExports.uniq(invalidChars).map((c) => {
+        if (c === " ") {
+          return "space";
+        }
+        return c;
+      }).slice(0, 100).join(", ")} `
     );
   }
-  if (typeof window !== "undefined" && window.toastr && warnings.length) {
-    warnings.forEach((warning) => {
-      window.toastr.warning(warning);
-    });
-  }
+  showWarnings(warnings);
   return [sanitizedVal, warnings];
 }
 __name(filterSequenceString, "filterSequenceString");
@@ -11668,12 +11683,12 @@ const calcTmMethods = {
   // Monovalent salt concentration. 50mM is typical for PCR.
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
-   * @param  {String} sequence The DNA sequence to use.
-   * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-   * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-   * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-   * @return {Double} Temperature for the given sequence, in Celsius.
+   * sequence - The DNA sequence to use.
+   * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+   * A - Helix initation for deltaS. Defaults to -10.8.
+   * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * return - Temperature for the given sequence, in Celsius.
    */
   calculateTemperature: function(sequence, type, A, R, C, Na) {
     if (typeof type === "undefined") {
@@ -19772,7 +19787,7 @@ function flattenSequenceArray(parsingResultArray, opts) {
   return parsingResultArray;
 }
 __name(flattenSequenceArray, "flattenSequenceArray");
-function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd) {
+function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd, isCircular, sequenceLength) {
   locStr = locStr.trim();
   const locArr = [];
   locStr.replace(/(\d+)/g, function(string, match) {
@@ -19793,6 +19808,19 @@ function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive
       isProtein ? convertAACaretPositionOrRangeToDna(location) : location
     );
   }
+  if (isCircular) {
+    for (let i = 0; i < locArray.length; i += 2) {
+      const firstFeature = locArray[i];
+      const secondFeature = locArray[i + 1];
+      if (firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) && secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)) {
+        locArray[i] = {
+          start: firstFeature.start,
+          end: secondFeature.end
+        };
+        locArray.splice(i + 1, 1);
+      }
+    }
+  }
   return locArray;
 }
 __name(parseFeatureLocation, "parseFeatureLocation");
@@ -20126,7 +20154,9 @@ function genbankToJson(string, options = {}) {
             line.trim(),
             options.isProtein,
             inclusive1BasedStart,
-            inclusive1BasedEnd
+            inclusive1BasedEnd,
+            result.parsedSequence.circular,
+            result.parsedSequence.sequence.length
           )
         );
         lastLineWasLocation = true;
@@ -20159,7 +20189,9 @@ function genbankToJson(string, options = {}) {
             val2,
             options.isProtein,
             inclusive1BasedStart,
-            inclusive1BasedEnd
+            inclusive1BasedEnd,
+            result.parsedSequence.circular,
+            result.parsedSequence.sequence.length
           )
         );
         lastLineWasLocation = true;
@@ -21047,7 +21079,6 @@ const util$1 = util$4;
 const xmlNode = xmlNode$1;
 const readDocType = DocTypeReader;
 const toNumber = strnum;
-"<((!\\[CDATA\\[([\\s\\S]*?)(]]>))|((NAME:)?(NAME))([^>]*)>|((\\/)(NAME)\\s*>))([^<]*)".replace(/NAME/g, util$1.nameRegexp);
 let OrderedObjParser$1 = (_a = class {
   constructor(options) {
     this.options = options;
@@ -21261,18 +21292,19 @@ const parseXml = /* @__PURE__ */ __name(function(xmlData) {
         const closeIndex = findClosingIndex(xmlData, "]]>", i, "CDATA is not closed.") - 2;
         const tagExp = xmlData.substring(i + 9, closeIndex);
         textData = this.saveTextToParentTag(textData, currentNode, jPath);
+        let val2 = this.parseTextData(tagExp, currentNode.tagname, jPath, true, false, true, true);
+        if (val2 == void 0)
+          val2 = "";
         if (this.options.cdataPropName) {
           currentNode.add(this.options.cdataPropName, [{ [this.options.textNodeName]: tagExp }]);
         } else {
-          let val2 = this.parseTextData(tagExp, currentNode.tagname, jPath, true, false, true);
-          if (val2 == void 0)
-            val2 = "";
           currentNode.add(this.options.textNodeName, val2);
         }
         i = closeIndex + 2;
       } else {
         let result = readTagExp(xmlData, i, this.options.removeNSPrefix);
         let tagName = result.tagName;
+        const rawTagName = result.rawTagName;
         let tagExp = result.tagExp;
         let attrExpPresent = result.attrExpPresent;
         let closeIndex = result.closeIndex;
@@ -21299,9 +21331,9 @@ const parseXml = /* @__PURE__ */ __name(function(xmlData) {
           } else if (this.options.unpairedTags.indexOf(tagName) !== -1) {
             i = result.closeIndex;
           } else {
-            const result2 = this.readStopNodeData(xmlData, tagName, closeIndex + 1);
+            const result2 = this.readStopNodeData(xmlData, rawTagName, closeIndex + 1);
             if (!result2)
-              throw new Error(`Unexpected end of ${tagName}`);
+              throw new Error(`Unexpected end of ${rawTagName}`);
             i = result2.i;
             tagContent = result2.tagContent;
           }
@@ -21463,9 +21495,10 @@ function readTagExp(xmlData, i, removeNSPrefix, closingChar = ">") {
   let tagName = tagExp;
   let attrExpPresent = true;
   if (separatorIndex !== -1) {
-    tagName = tagExp.substr(0, separatorIndex).replace(/\s\s*$/, "");
-    tagExp = tagExp.substr(separatorIndex + 1);
+    tagName = tagExp.substring(0, separatorIndex);
+    tagExp = tagExp.substring(separatorIndex + 1).trimStart();
   }
+  const rawTagName = tagName;
   if (removeNSPrefix) {
     const colonIndex = tagName.indexOf(":");
     if (colonIndex !== -1) {
@@ -21477,7 +21510,8 @@ function readTagExp(xmlData, i, removeNSPrefix, closingChar = ">") {
     tagName,
     tagExp,
     closeIndex,
-    attrExpPresent
+    attrExpPresent,
+    rawTagName
   };
 }
 __name(readTagExp, "readTagExp");
@@ -21707,6 +21741,8 @@ function arrToStr(arr, options, jPath, indentation) {
   for (let i = 0; i < arr.length; i++) {
     const tagObj = arr[i];
     const tagName = propName(tagObj);
+    if (tagName === void 0)
+      continue;
     let newJPath = "";
     if (jPath.length === 0)
       newJPath = tagName;
@@ -21778,6 +21814,8 @@ function propName(obj) {
   const keys = Object.keys(obj);
   for (let i = 0; i < keys.length; i++) {
     const key = keys[i];
+    if (!obj.hasOwnProperty(key))
+      continue;
     if (key !== ":@")
       return key;
   }
@@ -21787,6 +21825,8 @@ function attr_to_str(attrMap, options) {
   let attrStr = "";
   if (attrMap && !options.ignoreAttributes) {
     for (let attr in attrMap) {
+      if (!attrMap.hasOwnProperty(attr))
+        continue;
       let attrVal = options.attributeValueProcessor(attr, attrMap[attr]);
       attrVal = replaceEntitiesValue(attrVal, options);
       if (attrVal === true && options.suppressBooleanAttributes) {
@@ -21895,6 +21935,8 @@ Builder.prototype.j2x = function(jObj, level) {
   let attrStr = "";
   let val2 = "";
   for (let key in jObj) {
+    if (!Object.prototype.hasOwnProperty.call(jObj, key))
+      continue;
     if (typeof jObj[key] === "undefined") {
       if (this.isAttribute(key)) {
         val2 += "";
@@ -30334,9 +30376,7 @@ var slc = /* @__PURE__ */ __name(function(v, s, e) {
     s = 0;
   if (e == null || e > v.length)
     e = v.length;
-  var n = new u8(e - s);
-  n.set(v.subarray(s, e));
-  return n;
+  return new u8(v.subarray(s, e));
 }, "slc");
 var ec = [
   "unexpected EOF",
@@ -30368,9 +30408,10 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
   var sl = dat.length, dl = dict ? dict.length : 0;
   if (!sl || st.f && !st.l)
     return buf || new u8(0);
-  var noBuf = !buf || st.i != 2;
+  var noBuf = !buf;
+  var resize = noBuf || st.i != 2;
   var noSt = st.i;
-  if (!buf)
+  if (noBuf)
     buf = new u8(sl * 3);
   var cbuf = /* @__PURE__ */ __name(function(l2) {
     var bl = buf.length;
@@ -30394,7 +30435,7 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
             err(0);
           break;
         }
-        if (noBuf)
+        if (resize)
           cbuf(bt + l);
         buf.set(dat.subarray(s, t), bt);
         st.b = bt += l, st.p = pos = t * 8, st.f = final;
@@ -30444,7 +30485,7 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
         break;
       }
     }
-    if (noBuf)
+    if (resize)
       cbuf(bt + 131072);
     var lms = (1 << lbt) - 1, dms = (1 << dbt) - 1;
     var lpos = pos;
@@ -30484,7 +30525,7 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
             err(0);
           break;
         }
-        if (noBuf)
+        if (resize)
           cbuf(bt + 131072);
         var end = bt + add;
         if (bt < dt) {
@@ -30494,20 +30535,15 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
           for (; bt < dend; ++bt)
             buf[bt] = dict[shift + bt];
         }
-        for (; bt < end; bt += 4) {
+        for (; bt < end; ++bt)
           buf[bt] = buf[bt - dt];
-          buf[bt + 1] = buf[bt + 1 - dt];
-          buf[bt + 2] = buf[bt + 2 - dt];
-          buf[bt + 3] = buf[bt + 3 - dt];
-        }
-        bt = end;
       }
     }
     st.l = lm, st.p = lpos, st.b = bt, st.f = final;
     if (lm)
       final = 1, st.m = lbt, st.d = dm, st.n = dbt;
   } while (!final);
-  return bt == buf.length ? buf : slc(buf, 0, bt);
+  return bt != buf.length && noBuf ? slc(buf, 0, bt) : buf.subarray(0, bt);
 }, "inflt");
 var et = /* @__PURE__ */ new u8(0);
 var b2 = /* @__PURE__ */ __name(function(d, b) {
@@ -32671,13 +32707,12 @@ function jsonToFasta(jsonSequence, options) {
     proteinSize,
     proteinSequence
   } = cleanedData;
-  options = options || {};
-  let seqToUse = sequence;
-  let sizeToUse = size;
-  if (isProtein && proteinSequence) {
-    seqToUse = proteinSequence;
-    sizeToUse = proteinSize;
-  }
+  options = __spreadValues({
+    sequence: isProtein && proteinSequence ? proteinSequence : sequence,
+    size: isProtein && proteinSequence ? proteinSize : size
+  }, options);
+  const seqToUse = options.sequence;
+  const sizeToUse = options.size;
   let fastaString = "";
   fastaString += `>${name || "Untitled Sequence"}|`;
   fastaString += "|" + sizeToUse;

package/index.mjs

@@ -991,7 +991,7 @@ lodash.exports;
         return new LodashWrapper(value);
       }
       __name(lodash2, "lodash");
-      var baseCreate = function() {
+      var baseCreate = /* @__PURE__ */ function() {
         function object() {
         }
         __name(object, "object");
@@ -4616,7 +4616,7 @@ lodash.exports;
       var gte = createRelationalOperation(function(value, other) {
         return value >= other;
       });
-      var isArguments = baseIsArguments(function() {
+      var isArguments = baseIsArguments(/* @__PURE__ */ function() {
         return arguments;
       }()) ? baseIsArguments : function(value) {
         return isObjectLike(value) && hasOwnProperty2.call(value, "callee") && !propertyIsEnumerable.call(value, "callee");
@@ -6167,7 +6167,7 @@ lodash.exports;
   }).call(commonjsGlobal);
 })(lodash, lodash.exports);
 var lodashExports = lodash.exports;
-const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
+const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
 const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
 const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
 const aminoAcidToDegenerateDnaMap = {
@@ -6882,7 +6882,7 @@ __name(requireEmpty, "requireEmpty");
         throw new TypeError("Cannot call a class as a function");
       }
     }, "classCallCheck");
-    var createClass = function() {
+    var createClass = /* @__PURE__ */ function() {
       function defineProperties(target, props) {
         for (var i = 0; i < props.length; i++) {
           var descriptor = props[i];
@@ -6944,7 +6944,7 @@ __name(requireEmpty, "requireEmpty");
       }
       return call && (typeof call === "object" || typeof call === "function") ? call : self2;
     }, "possibleConstructorReturn");
-    var slicedToArray = function() {
+    var slicedToArray = /* @__PURE__ */ function() {
       function sliceIterator(arr, i) {
         var _arr = [];
         var _n = true;
@@ -11272,6 +11272,20 @@ const annotationTypes = [
   "primers",
   "guides"
 ];
+let allWarnings = [];
+let makeToast = /* @__PURE__ */ __name(() => {
+  if (typeof window !== "undefined" && window.toastr && allWarnings.length) {
+    window.toastr.warning(lodashExports.uniq(allWarnings).join("\n"));
+  }
+  allWarnings = [];
+}, "makeToast");
+makeToast = lodashExports.debounce(makeToast, 200);
+function showWarnings(warnings) {
+  allWarnings = allWarnings.concat(warnings);
+  makeToast.cancel();
+  makeToast();
+}
+__name(showWarnings, "showWarnings");
 function filterSequenceString(sequenceString = "", {
   additionalValidChars = "",
   isOligo,
@@ -11319,14 +11333,15 @@ function filterSequenceString(sequenceString = "", {
   });
   if (sequenceString.length !== sanitizedVal.length) {
     warnings.push(
-      `${name ? `Sequence ${name}: ` : ""}Invalid character(s) detected and removed: ${invalidChars.slice(0, 100).join(", ")} `
+      `${name ? `Sequence ${name}: ` : ""}Invalid character(s) detected and removed: ${lodashExports.uniq(invalidChars).map((c) => {
+        if (c === " ") {
+          return "space";
+        }
+        return c;
+      }).slice(0, 100).join(", ")} `
     );
   }
-  if (typeof window !== "undefined" && window.toastr && warnings.length) {
-    warnings.forEach((warning) => {
-      window.toastr.warning(warning);
-    });
-  }
+  showWarnings(warnings);
   return [sanitizedVal, warnings];
 }
 __name(filterSequenceString, "filterSequenceString");
@@ -11666,12 +11681,12 @@ const calcTmMethods = {
   // Monovalent salt concentration. 50mM is typical for PCR.
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
-   * @param  {String} sequence The DNA sequence to use.
-   * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-   * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-   * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-   * @return {Double} Temperature for the given sequence, in Celsius.
+   * sequence - The DNA sequence to use.
+   * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+   * A - Helix initation for deltaS. Defaults to -10.8.
+   * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * return - Temperature for the given sequence, in Celsius.
    */
   calculateTemperature: function(sequence, type, A, R, C, Na) {
     if (typeof type === "undefined") {
@@ -19770,7 +19785,7 @@ function flattenSequenceArray(parsingResultArray, opts) {
   return parsingResultArray;
 }
 __name(flattenSequenceArray, "flattenSequenceArray");
-function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd) {
+function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd, isCircular, sequenceLength) {
   locStr = locStr.trim();
   const locArr = [];
   locStr.replace(/(\d+)/g, function(string, match) {
@@ -19791,6 +19806,19 @@ function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive
       isProtein ? convertAACaretPositionOrRangeToDna(location) : location
     );
   }
+  if (isCircular) {
+    for (let i = 0; i < locArray.length; i += 2) {
+      const firstFeature = locArray[i];
+      const secondFeature = locArray[i + 1];
+      if (firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) && secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)) {
+        locArray[i] = {
+          start: firstFeature.start,
+          end: secondFeature.end
+        };
+        locArray.splice(i + 1, 1);
+      }
+    }
+  }
   return locArray;
 }
 __name(parseFeatureLocation, "parseFeatureLocation");
@@ -20124,7 +20152,9 @@ function genbankToJson(string, options = {}) {
             line.trim(),
             options.isProtein,
             inclusive1BasedStart,
-            inclusive1BasedEnd
+            inclusive1BasedEnd,
+            result.parsedSequence.circular,
+            result.parsedSequence.sequence.length
           )
         );
         lastLineWasLocation = true;
@@ -20157,7 +20187,9 @@ function genbankToJson(string, options = {}) {
             val2,
             options.isProtein,
             inclusive1BasedStart,
-            inclusive1BasedEnd
+            inclusive1BasedEnd,
+            result.parsedSequence.circular,
+            result.parsedSequence.sequence.length
           )
         );
         lastLineWasLocation = true;
@@ -21045,7 +21077,6 @@ const util$1 = util$4;
 const xmlNode = xmlNode$1;
 const readDocType = DocTypeReader;
 const toNumber = strnum;
-"<((!\\[CDATA\\[([\\s\\S]*?)(]]>))|((NAME:)?(NAME))([^>]*)>|((\\/)(NAME)\\s*>))([^<]*)".replace(/NAME/g, util$1.nameRegexp);
 let OrderedObjParser$1 = (_a = class {
   constructor(options) {
     this.options = options;
@@ -21259,18 +21290,19 @@ const parseXml = /* @__PURE__ */ __name(function(xmlData) {
         const closeIndex = findClosingIndex(xmlData, "]]>", i, "CDATA is not closed.") - 2;
         const tagExp = xmlData.substring(i + 9, closeIndex);
         textData = this.saveTextToParentTag(textData, currentNode, jPath);
+        let val2 = this.parseTextData(tagExp, currentNode.tagname, jPath, true, false, true, true);
+        if (val2 == void 0)
+          val2 = "";
         if (this.options.cdataPropName) {
           currentNode.add(this.options.cdataPropName, [{ [this.options.textNodeName]: tagExp }]);
         } else {
-          let val2 = this.parseTextData(tagExp, currentNode.tagname, jPath, true, false, true);
-          if (val2 == void 0)
-            val2 = "";
           currentNode.add(this.options.textNodeName, val2);
         }
         i = closeIndex + 2;
       } else {
         let result = readTagExp(xmlData, i, this.options.removeNSPrefix);
         let tagName = result.tagName;
+        const rawTagName = result.rawTagName;
         let tagExp = result.tagExp;
         let attrExpPresent = result.attrExpPresent;
         let closeIndex = result.closeIndex;
@@ -21297,9 +21329,9 @@ const parseXml = /* @__PURE__ */ __name(function(xmlData) {
           } else if (this.options.unpairedTags.indexOf(tagName) !== -1) {
             i = result.closeIndex;
           } else {
-            const result2 = this.readStopNodeData(xmlData, tagName, closeIndex + 1);
+            const result2 = this.readStopNodeData(xmlData, rawTagName, closeIndex + 1);
             if (!result2)
-              throw new Error(`Unexpected end of ${tagName}`);
+              throw new Error(`Unexpected end of ${rawTagName}`);
             i = result2.i;
             tagContent = result2.tagContent;
           }
@@ -21461,9 +21493,10 @@ function readTagExp(xmlData, i, removeNSPrefix, closingChar = ">") {
   let tagName = tagExp;
   let attrExpPresent = true;
   if (separatorIndex !== -1) {
-    tagName = tagExp.substr(0, separatorIndex).replace(/\s\s*$/, "");
-    tagExp = tagExp.substr(separatorIndex + 1);
+    tagName = tagExp.substring(0, separatorIndex);
+    tagExp = tagExp.substring(separatorIndex + 1).trimStart();
   }
+  const rawTagName = tagName;
   if (removeNSPrefix) {
     const colonIndex = tagName.indexOf(":");
     if (colonIndex !== -1) {
@@ -21475,7 +21508,8 @@ function readTagExp(xmlData, i, removeNSPrefix, closingChar = ">") {
     tagName,
     tagExp,
     closeIndex,
-    attrExpPresent
+    attrExpPresent,
+    rawTagName
   };
 }
 __name(readTagExp, "readTagExp");
@@ -21705,6 +21739,8 @@ function arrToStr(arr, options, jPath, indentation) {
   for (let i = 0; i < arr.length; i++) {
     const tagObj = arr[i];
     const tagName = propName(tagObj);
+    if (tagName === void 0)
+      continue;
     let newJPath = "";
     if (jPath.length === 0)
       newJPath = tagName;
@@ -21776,6 +21812,8 @@ function propName(obj) {
   const keys = Object.keys(obj);
   for (let i = 0; i < keys.length; i++) {
     const key = keys[i];
+    if (!obj.hasOwnProperty(key))
+      continue;
     if (key !== ":@")
       return key;
   }
@@ -21785,6 +21823,8 @@ function attr_to_str(attrMap, options) {
   let attrStr = "";
   if (attrMap && !options.ignoreAttributes) {
     for (let attr in attrMap) {
+      if (!attrMap.hasOwnProperty(attr))
+        continue;
       let attrVal = options.attributeValueProcessor(attr, attrMap[attr]);
       attrVal = replaceEntitiesValue(attrVal, options);
       if (attrVal === true && options.suppressBooleanAttributes) {
@@ -21893,6 +21933,8 @@ Builder.prototype.j2x = function(jObj, level) {
   let attrStr = "";
   let val2 = "";
   for (let key in jObj) {
+    if (!Object.prototype.hasOwnProperty.call(jObj, key))
+      continue;
     if (typeof jObj[key] === "undefined") {
       if (this.isAttribute(key)) {
         val2 += "";
@@ -30332,9 +30374,7 @@ var slc = /* @__PURE__ */ __name(function(v, s, e) {
     s = 0;
   if (e == null || e > v.length)
     e = v.length;
-  var n = new u8(e - s);
-  n.set(v.subarray(s, e));
-  return n;
+  return new u8(v.subarray(s, e));
 }, "slc");
 var ec = [
   "unexpected EOF",
@@ -30366,9 +30406,10 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
   var sl = dat.length, dl = dict ? dict.length : 0;
   if (!sl || st.f && !st.l)
     return buf || new u8(0);
-  var noBuf = !buf || st.i != 2;
+  var noBuf = !buf;
+  var resize = noBuf || st.i != 2;
   var noSt = st.i;
-  if (!buf)
+  if (noBuf)
     buf = new u8(sl * 3);
   var cbuf = /* @__PURE__ */ __name(function(l2) {
     var bl = buf.length;
@@ -30392,7 +30433,7 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
             err(0);
           break;
         }
-        if (noBuf)
+        if (resize)
           cbuf(bt + l);
         buf.set(dat.subarray(s, t), bt);
         st.b = bt += l, st.p = pos = t * 8, st.f = final;
@@ -30442,7 +30483,7 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
         break;
       }
     }
-    if (noBuf)
+    if (resize)
       cbuf(bt + 131072);
     var lms = (1 << lbt) - 1, dms = (1 << dbt) - 1;
     var lpos = pos;
@@ -30482,7 +30523,7 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
             err(0);
           break;
         }
-        if (noBuf)
+        if (resize)
           cbuf(bt + 131072);
         var end = bt + add;
         if (bt < dt) {
@@ -30492,20 +30533,15 @@ var inflt = /* @__PURE__ */ __name(function(dat, st, buf, dict) {
           for (; bt < dend; ++bt)
             buf[bt] = dict[shift + bt];
         }
-        for (; bt < end; bt += 4) {
+        for (; bt < end; ++bt)
           buf[bt] = buf[bt - dt];
-          buf[bt + 1] = buf[bt + 1 - dt];
-          buf[bt + 2] = buf[bt + 2 - dt];
-          buf[bt + 3] = buf[bt + 3 - dt];
-        }
-        bt = end;
       }
     }
     st.l = lm, st.p = lpos, st.b = bt, st.f = final;
     if (lm)
       final = 1, st.m = lbt, st.d = dm, st.n = dbt;
   } while (!final);
-  return bt == buf.length ? buf : slc(buf, 0, bt);
+  return bt != buf.length && noBuf ? slc(buf, 0, bt) : buf.subarray(0, bt);
 }, "inflt");
 var et = /* @__PURE__ */ new u8(0);
 var b2 = /* @__PURE__ */ __name(function(d, b) {
@@ -32669,13 +32705,12 @@ function jsonToFasta(jsonSequence, options) {
     proteinSize,
     proteinSequence
   } = cleanedData;
-  options = options || {};
-  let seqToUse = sequence;
-  let sizeToUse = size;
-  if (isProtein && proteinSequence) {
-    seqToUse = proteinSequence;
-    sizeToUse = proteinSize;
-  }
+  options = __spreadValues({
+    sequence: isProtein && proteinSequence ? proteinSequence : sequence,
+    size: isProtein && proteinSequence ? proteinSize : size
+  }, options);
+  const seqToUse = options.sequence;
+  const sizeToUse = options.size;
   let fastaString = "";
   fastaString += `>${name || "Untitled Sequence"}|`;
   fastaString += "|" + sizeToUse;

package/index.umd.js

@@ -1,4 +1,7 @@
-var __defProp = Object.defineProperty;
+(function(global2, factory) {
+  typeof exports === "object" && typeof module !== "undefined" ? factory(exports) : typeof define === "function" && define.amd ? define(["exports"], factory) : (global2 = typeof globalThis !== "undefined" ? globalThis : global2 || self, factory(global2.bioParsers = {}));
+})(this, function(exports2) {
+  "use strict";var __defProp = Object.defineProperty;
 var __defProps = Object.defineProperties;
 var __getOwnPropDescs = Object.getOwnPropertyDescriptors;
 var __getOwnPropSymbols = Object.getOwnPropertySymbols;
@@ -39,11 +42,8 @@ var __async = (__this, __arguments, generator) => {
     step((generator = generator.apply(__this, __arguments)).next());
   });
 };
-(function(global2, factory) {
-  typeof exports === "object" && typeof module !== "undefined" ? factory(exports) : typeof define === "function" && define.amd ? define(["exports"], factory) : (global2 = typeof globalThis !== "undefined" ? globalThis : global2 || self, factory(global2.bioParsers = {}));
-})(this, function(exports2) {
+
   var _a2, _b2;
-  "use strict";
   const untitledSequenceName = "Untitled Sequence";
   const gbDivisions = {
     // https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#GenBankDivisionB
@@ -995,7 +995,7 @@ var __async = (__this, __arguments, generator) => {
           return new LodashWrapper(value);
         }
         __name(lodash2, "lodash");
-        var baseCreate = function() {
+        var baseCreate = /* @__PURE__ */ function() {
           function object() {
           }
           __name(object, "object");
@@ -4620,7 +4620,7 @@ var __async = (__this, __arguments, generator) => {
         var gte = createRelationalOperation(function(value, other) {
           return value >= other;
         });
-        var isArguments = baseIsArguments(function() {
+        var isArguments = baseIsArguments(/* @__PURE__ */ function() {
           return arguments;
         }()) ? baseIsArguments : function(value) {
           return isObjectLike(value) && hasOwnProperty2.call(value, "callee") && !propertyIsEnumerable.call(value, "callee");
@@ -6171,7 +6171,7 @@ var __async = (__this, __arguments, generator) => {
     }).call(commonjsGlobal);
   })(lodash, lodash.exports);
   var lodashExports = lodash.exports;
-  const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
+  const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
   const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
   const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
   const aminoAcidToDegenerateDnaMap = {
@@ -6886,7 +6886,7 @@ var __async = (__this, __arguments, generator) => {
           throw new TypeError("Cannot call a class as a function");
         }
       }, "classCallCheck");
-      var createClass = function() {
+      var createClass = /* @__PURE__ */ function() {
         function defineProperties(target, props) {
           for (var i2 = 0; i2 < props.length; i2++) {
             var descriptor = props[i2];
@@ -6948,7 +6948,7 @@ var __async = (__this, __arguments, generator) => {
         }
         return call && (typeof call === "object" || typeof call === "function") ? call : self2;
       }, "possibleConstructorReturn");
-      var slicedToArray = function() {
+      var slicedToArray = /* @__PURE__ */ function() {
         function sliceIterator(arr, i2) {
           var _arr = [];
           var _n = true;
@@ -11276,6 +11276,20 @@ var __async = (__this, __arguments, generator) => {
     "primers",
     "guides"
   ];
+  let allWarnings = [];
+  let makeToast = /* @__PURE__ */ __name(() => {
+    if (typeof window !== "undefined" && window.toastr && allWarnings.length) {
+      window.toastr.warning(lodashExports.uniq(allWarnings).join("\n"));
+    }
+    allWarnings = [];
+  }, "makeToast");
+  makeToast = lodashExports.debounce(makeToast, 200);
+  function showWarnings(warnings) {
+    allWarnings = allWarnings.concat(warnings);
+    makeToast.cancel();
+    makeToast();
+  }
+  __name(showWarnings, "showWarnings");
   function filterSequenceString(sequenceString = "", {
     additionalValidChars = "",
     isOligo,
@@ -11323,14 +11337,15 @@ var __async = (__this, __arguments, generator) => {
     });
     if (sequenceString.length !== sanitizedVal.length) {
       warnings.push(
-        `${name2 ? `Sequence ${name2}: ` : ""}Invalid character(s) detected and removed: ${invalidChars.slice(0, 100).join(", ")} `
+        `${name2 ? `Sequence ${name2}: ` : ""}Invalid character(s) detected and removed: ${lodashExports.uniq(invalidChars).map((c) => {
+          if (c === " ") {
+            return "space";
+          }
+          return c;
+        }).slice(0, 100).join(", ")} `
       );
     }
-    if (typeof window !== "undefined" && window.toastr && warnings.length) {
-      warnings.forEach((warning) => {
-        window.toastr.warning(warning);
-      });
-    }
+    showWarnings(warnings);
     return [sanitizedVal, warnings];
   }
   __name(filterSequenceString, "filterSequenceString");
@@ -11670,12 +11685,12 @@ var __async = (__this, __arguments, generator) => {
     // Monovalent salt concentration. 50mM is typical for PCR.
     /**
      * Calculates temperature for DNA sequence using a given algorithm.
-     * @param  {String} sequence The DNA sequence to use.
-     * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-     * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-     * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-     * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-     * @return {Double} Temperature for the given sequence, in Celsius.
+     * sequence - The DNA sequence to use.
+     * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+     * A - Helix initation for deltaS. Defaults to -10.8.
+     * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+     * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+     * return - Temperature for the given sequence, in Celsius.
      */
     calculateTemperature: function(sequence, type, A, R, C, Na) {
       if (typeof type === "undefined") {
@@ -19774,7 +19789,7 @@ var __async = (__this, __arguments, generator) => {
     return parsingResultArray;
   }
   __name(flattenSequenceArray, "flattenSequenceArray");
-  function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd) {
+  function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd, isCircular, sequenceLength) {
     locStr = locStr.trim();
     const locArr = [];
     locStr.replace(/(\d+)/g, function(string, match) {
@@ -19795,6 +19810,19 @@ var __async = (__this, __arguments, generator) => {
         isProtein ? convertAACaretPositionOrRangeToDna(location) : location
       );
     }
+    if (isCircular) {
+      for (let i2 = 0; i2 < locArray.length; i2 += 2) {
+        const firstFeature = locArray[i2];
+        const secondFeature = locArray[i2 + 1];
+        if (firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) && secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)) {
+          locArray[i2] = {
+            start: firstFeature.start,
+            end: secondFeature.end
+          };
+          locArray.splice(i2 + 1, 1);
+        }
+      }
+    }
     return locArray;
   }
   __name(parseFeatureLocation, "parseFeatureLocation");
@@ -20128,7 +20156,9 @@ var __async = (__this, __arguments, generator) => {
               line.trim(),
               options.isProtein,
               inclusive1BasedStart,
-              inclusive1BasedEnd
+              inclusive1BasedEnd,
+              result.parsedSequence.circular,
+              result.parsedSequence.sequence.length
             )
           );
           lastLineWasLocation = true;
@@ -20161,7 +20191,9 @@ var __async = (__this, __arguments, generator) => {
               val2,
               options.isProtein,
               inclusive1BasedStart,
-              inclusive1BasedEnd
+              inclusive1BasedEnd,
+              result.parsedSequence.circular,
+              result.parsedSequence.sequence.length
             )
           );
           lastLineWasLocation = true;
@@ -21049,7 +21081,6 @@ var __async = (__this, __arguments, generator) => {
   const xmlNode = xmlNode$1;
   const readDocType = DocTypeReader;
   const toNumber = strnum;
-  "<((!\\[CDATA\\[([\\s\\S]*?)(]]>))|((NAME:)?(NAME))([^>]*)>|((\\/)(NAME)\\s*>))([^<]*)".replace(/NAME/g, util$1.nameRegexp);
   let OrderedObjParser$1 = (_a2 = class {
     constructor(options) {
       this.options = options;
@@ -21263,18 +21294,19 @@ var __async = (__this, __arguments, generator) => {
           const closeIndex = findClosingIndex(xmlData, "]]>", i2, "CDATA is not closed.") - 2;
           const tagExp = xmlData.substring(i2 + 9, closeIndex);
           textData = this.saveTextToParentTag(textData, currentNode, jPath);
+          let val2 = this.parseTextData(tagExp, currentNode.tagname, jPath, true, false, true, true);
+          if (val2 == void 0)
+            val2 = "";
           if (this.options.cdataPropName) {
             currentNode.add(this.options.cdataPropName, [{ [this.options.textNodeName]: tagExp }]);
           } else {
-            let val2 = this.parseTextData(tagExp, currentNode.tagname, jPath, true, false, true);
-            if (val2 == void 0)
-              val2 = "";
             currentNode.add(this.options.textNodeName, val2);
           }
           i2 = closeIndex + 2;
         } else {
           let result = readTagExp(xmlData, i2, this.options.removeNSPrefix);
           let tagName = result.tagName;
+          const rawTagName = result.rawTagName;
           let tagExp = result.tagExp;
           let attrExpPresent = result.attrExpPresent;
           let closeIndex = result.closeIndex;
@@ -21301,9 +21333,9 @@ var __async = (__this, __arguments, generator) => {
             } else if (this.options.unpairedTags.indexOf(tagName) !== -1) {
               i2 = result.closeIndex;
             } else {
-              const result2 = this.readStopNodeData(xmlData, tagName, closeIndex + 1);
+              const result2 = this.readStopNodeData(xmlData, rawTagName, closeIndex + 1);
               if (!result2)
-                throw new Error(`Unexpected end of ${tagName}`);
+                throw new Error(`Unexpected end of ${rawTagName}`);
               i2 = result2.i;
               tagContent = result2.tagContent;
             }
@@ -21465,9 +21497,10 @@ var __async = (__this, __arguments, generator) => {
     let tagName = tagExp;
     let attrExpPresent = true;
     if (separatorIndex !== -1) {
-      tagName = tagExp.substr(0, separatorIndex).replace(/\s\s*$/, "");
-      tagExp = tagExp.substr(separatorIndex + 1);
+      tagName = tagExp.substring(0, separatorIndex);
+      tagExp = tagExp.substring(separatorIndex + 1).trimStart();
     }
+    const rawTagName = tagName;
     if (removeNSPrefix) {
       const colonIndex = tagName.indexOf(":");
       if (colonIndex !== -1) {
@@ -21479,7 +21512,8 @@ var __async = (__this, __arguments, generator) => {
       tagName,
       tagExp,
       closeIndex,
-      attrExpPresent
+      attrExpPresent,
+      rawTagName
     };
   }
   __name(readTagExp, "readTagExp");
@@ -21709,6 +21743,8 @@ var __async = (__this, __arguments, generator) => {
     for (let i2 = 0; i2 < arr.length; i2++) {
       const tagObj = arr[i2];
       const tagName = propName(tagObj);
+      if (tagName === void 0)
+        continue;
       let newJPath = "";
       if (jPath.length === 0)
         newJPath = tagName;
@@ -21780,6 +21816,8 @@ var __async = (__this, __arguments, generator) => {
     const keys = Object.keys(obj);
     for (let i2 = 0; i2 < keys.length; i2++) {
       const key = keys[i2];
+      if (!obj.hasOwnProperty(key))
+        continue;
       if (key !== ":@")
         return key;
     }
@@ -21789,6 +21827,8 @@ var __async = (__this, __arguments, generator) => {
     let attrStr = "";
     if (attrMap && !options.ignoreAttributes) {
       for (let attr in attrMap) {
+        if (!attrMap.hasOwnProperty(attr))
+          continue;
         let attrVal = options.attributeValueProcessor(attr, attrMap[attr]);
         attrVal = replaceEntitiesValue(attrVal, options);
         if (attrVal === true && options.suppressBooleanAttributes) {
@@ -21897,6 +21937,8 @@ var __async = (__this, __arguments, generator) => {
     let attrStr = "";
     let val2 = "";
     for (let key in jObj) {
+      if (!Object.prototype.hasOwnProperty.call(jObj, key))
+        continue;
       if (typeof jObj[key] === "undefined") {
         if (this.isAttribute(key)) {
           val2 += "";
@@ -30336,9 +30378,7 @@ ${seq.sequence}
       s = 0;
     if (e == null || e > v.length)
       e = v.length;
-    var n = new u8(e - s);
-    n.set(v.subarray(s, e));
-    return n;
+    return new u8(v.subarray(s, e));
   }, "slc");
   var ec = [
     "unexpected EOF",
@@ -30370,9 +30410,10 @@ ${seq.sequence}
     var sl = dat.length, dl = dict ? dict.length : 0;
     if (!sl || st.f && !st.l)
       return buf || new u8(0);
-    var noBuf = !buf || st.i != 2;
+    var noBuf = !buf;
+    var resize = noBuf || st.i != 2;
     var noSt = st.i;
-    if (!buf)
+    if (noBuf)
       buf = new u8(sl * 3);
     var cbuf = /* @__PURE__ */ __name(function(l2) {
       var bl = buf.length;
@@ -30396,7 +30437,7 @@ ${seq.sequence}
               err(0);
             break;
           }
-          if (noBuf)
+          if (resize)
             cbuf(bt + l);
           buf.set(dat.subarray(s, t), bt);
           st.b = bt += l, st.p = pos = t * 8, st.f = final;
@@ -30446,7 +30487,7 @@ ${seq.sequence}
           break;
         }
       }
-      if (noBuf)
+      if (resize)
         cbuf(bt + 131072);
       var lms = (1 << lbt) - 1, dms = (1 << dbt) - 1;
       var lpos = pos;
@@ -30486,7 +30527,7 @@ ${seq.sequence}
               err(0);
             break;
           }
-          if (noBuf)
+          if (resize)
             cbuf(bt + 131072);
           var end = bt + add;
           if (bt < dt) {
@@ -30496,20 +30537,15 @@ ${seq.sequence}
             for (; bt < dend; ++bt)
               buf[bt] = dict[shift + bt];
           }
-          for (; bt < end; bt += 4) {
+          for (; bt < end; ++bt)
             buf[bt] = buf[bt - dt];
-            buf[bt + 1] = buf[bt + 1 - dt];
-            buf[bt + 2] = buf[bt + 2 - dt];
-            buf[bt + 3] = buf[bt + 3 - dt];
-          }
-          bt = end;
         }
       }
       st.l = lm, st.p = lpos, st.b = bt, st.f = final;
       if (lm)
         final = 1, st.m = lbt, st.d = dm, st.n = dbt;
     } while (!final);
-    return bt == buf.length ? buf : slc(buf, 0, bt);
+    return bt != buf.length && noBuf ? slc(buf, 0, bt) : buf.subarray(0, bt);
   }, "inflt");
   var et = /* @__PURE__ */ new u8(0);
   var b2 = /* @__PURE__ */ __name(function(d, b) {
@@ -32673,13 +32709,12 @@ ${seq.sequence}
       proteinSize,
       proteinSequence
     } = cleanedData;
-    options = options || {};
-    let seqToUse = sequence;
-    let sizeToUse = size;
-    if (isProtein && proteinSequence) {
-      seqToUse = proteinSequence;
-      sizeToUse = proteinSize;
-    }
+    options = __spreadValues({
+      sequence: isProtein && proteinSequence ? proteinSequence : sequence,
+      size: isProtein && proteinSequence ? proteinSize : size
+    }, options);
+    const seqToUse = options.sequence;
+    const sizeToUse = options.size;
     let fastaString = "";
     fastaString += `>${name2 || "Untitled Sequence"}|`;
     fastaString += "|" + sizeToUse;

package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.9",
+  "version": "0.4.11",
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.15",
+    "@teselagen/sequence-utils": "0.3.20",
     "@teselagen/range-utils": "0.3.7",
     "@gmod/gff": "^1.2.1",
     "buffer": "^6.0.3",

package/src/genbankToJson.js

@@ -12,7 +12,9 @@ export function parseFeatureLocation(
   locStr,
   isProtein,
   inclusive1BasedStart,
-  inclusive1BasedEnd
+  inclusive1BasedEnd,
+  isCircular,
+  sequenceLength
 ) {
   locStr = locStr.trim();
   const locArr = [];
@@ -39,6 +41,30 @@ export function parseFeatureLocation(
       isProtein ? convertAACaretPositionOrRangeToDna(location) : location
     );
   }
+  // In genbank files, origin-spanning features are represented as follows:
+  // complement(join(490883..490885,1..879)) (for a circular sequence of length 490885)
+  // Then, for locations in locArray we check if there is a feature that ends at sequenceLength
+  // joined with a feature that starts at 1. If so, we merge them into a single feature.
+  // (see https://github.com/TeselaGen/tg-oss/issues/35)
+
+  if (isCircular) {
+    // Iterate by pairs of features
+    for (let i = 0; i < locArray.length; i += 2) {
+      const firstFeature = locArray[i];
+      const secondFeature = locArray[i + 1];
+      if (
+        firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) &&
+        secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)
+      ) {
+        // Merge the two features
+        locArray[i] = {
+          start: firstFeature.start,
+          end: secondFeature.end
+        };
+        locArray.splice(i + 1, 1);
+      }
+    }
+  }
   return locArray;
 }
 
@@ -468,7 +494,9 @@ function genbankToJson(string, options = {}) {
             line.trim(),
             options.isProtein,
             inclusive1BasedStart,
-            inclusive1BasedEnd
+            inclusive1BasedEnd,
+            result.parsedSequence.circular,
+            result.parsedSequence.sequence.length
           )
         );
         lastLineWasLocation = true;
@@ -513,7 +541,9 @@ function genbankToJson(string, options = {}) {
             val,
             options.isProtein,
             inclusive1BasedStart,
-            inclusive1BasedEnd
+            inclusive1BasedEnd,
+            result.parsedSequence.circular,
+            result.parsedSequence.sequence.length
           )
         );
         lastLineWasLocation = true;
@@ -663,8 +693,8 @@ function genbankToJson(string, options = {}) {
         feat.notes.direction[0].toUpperCase() === "BOTH"
           ? "BOTH"
           : feat.notes.direction[0].toUpperCase() === "NONE"
-          ? "NONE"
-          : undefined;
+            ? "NONE"
+            : undefined;
       delete feat.notes.direction;
     }
     return feat;

package/src/jsonToFasta.js

@@ -14,13 +14,13 @@ export default function jsonToFasta(jsonSequence, options) {
     proteinSequence
   } = cleanedData;
 
-  options = options || {};
-  let seqToUse = sequence;
-  let sizeToUse = size;
-  if (isProtein && proteinSequence) {
-    seqToUse = proteinSequence;
-    sizeToUse = proteinSize;
-  }
+  options = {
+    sequence: isProtein && proteinSequence ? proteinSequence : sequence,
+    size: isProtein && proteinSequence ? proteinSize : size,
+    ...options
+  };
+  const seqToUse = options.sequence;
+  const sizeToUse = options.size;
   // options.reformatSeqName = options.reformatSeqName === false ? false : true;
   let fastaString = "";
   fastaString += `>${name || "Untitled Sequence"}|`;