@teselagen/bio-parsers 0.3.8 → 0.3.10

package/index.js

@@ -6283,8 +6283,8 @@ function getOverlapsOfPotentiallyCircularRanges(rangeA, rangeB, maxRangeLength,
     maxRangeLength
   );
   let overlaps = [];
-  normalizedRangeA.forEach(function(nonCircularRangeA, iA) {
-    normalizedRangeB.forEach(function(nonCircularRangeB, iB) {
+  normalizedRangeA.forEach(function(nonCircularRangeA) {
+    normalizedRangeB.forEach(function(nonCircularRangeB) {
       const overlap = getOverlapOfNonCircularRanges(
         nonCircularRangeA,
         nonCircularRangeB
@@ -6296,7 +6296,7 @@ function getOverlapsOfPotentiallyCircularRanges(rangeA, rangeB, maxRangeLength,
   });
   if (joinIfPossible && normalizedRangeA.length === 2 && normalizedRangeB.length === 2 && maxRangeLength) {
     const joinedOverlap = {};
-    overlaps = lodashExports.flatMap(overlaps, (o, i) => {
+    overlaps = lodashExports.flatMap(overlaps, (o) => {
       if (o.start === 0) {
         joinedOverlap.end = o.end;
         return [];
@@ -6394,12 +6394,14 @@ function trimRangeByAnotherRange(rangeToBeTrimmed, trimmingRange, sequenceLength
     });
     splitRangesToBeTrimmed[index] = nonCircularRangeToBeTrimmed;
   });
-  const outputSplitRanges = splitRangesToBeTrimmed.filter(function(trimmedRange) {
-    if (trimmedRange) {
-      return true;
+  const outputSplitRanges = splitRangesToBeTrimmed.filter(
+    function(trimmedRange) {
+      if (trimmedRange) {
+        return true;
+      }
+      return false;
     }
-    return false;
-  });
+  );
   let outputTrimmedRange;
   if (outputSplitRanges.length < 0)
     ;
@@ -6449,8 +6451,14 @@ function normalizePositionByRangeLength(pPosition, sequenceLength, isInBetweenPo
 __name(normalizePositionByRangeLength, "normalizePositionByRangeLength");
 function translateRange(rangeToBeAdjusted, translateBy, rangeLength) {
   return lodashExports.assign({}, rangeToBeAdjusted, {
-    start: normalizePositionByRangeLength(rangeToBeAdjusted.start + translateBy, rangeLength),
-    end: normalizePositionByRangeLength(rangeToBeAdjusted.end + translateBy, rangeLength)
+    start: normalizePositionByRangeLength(
+      rangeToBeAdjusted.start + translateBy,
+      rangeLength
+    ),
+    end: normalizePositionByRangeLength(
+      rangeToBeAdjusted.end + translateBy,
+      rangeLength
+    )
   });
 }
 __name(translateRange, "translateRange");
@@ -10767,7 +10775,7 @@ const proteinAlphabet = {
     hydrophobicity: 1.8,
     colorByFamily: "#00FFFF",
     color: "hsl(327.3, 100%, 69%)",
-    mass: 89.1
+    mass: 71.0779
   },
   R: {
     value: "R",
@@ -10776,7 +10784,7 @@ const proteinAlphabet = {
     hydrophobicity: -4.5,
     colorByFamily: "#FFC0CB",
     color: "hsl(258.1, 100%, 69%)",
-    mass: 174.2
+    mass: 156.18568
   },
   N: {
     value: "N",
@@ -10785,7 +10793,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.5,
     colorByFamily: "#D3D3D3",
     color: "hsl(268.9, 100%, 69%)",
-    mass: 132.1
+    mass: 114.10264
   },
   D: {
     value: "D",
@@ -10794,7 +10802,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.5,
     colorByFamily: "#EE82EE",
     color: "hsl(268.9, 100%, 69%)",
-    mass: 133.1
+    mass: 115.0874
   },
   C: {
     value: "C",
@@ -10803,7 +10811,7 @@ const proteinAlphabet = {
     hydrophobicity: 2.5,
     colorByFamily: "#FFFF00",
     color: "hsl(335.1, 100%, 69%)",
-    mass: 121.2
+    mass: 103.1429
   },
   E: {
     value: "E",
@@ -10812,7 +10820,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.5,
     colorByFamily: "#EE82EE",
     color: "hsl(268.9, 100%, 69%)",
-    mass: 147.1
+    mass: 129.11398
   },
   Q: {
     value: "Q",
@@ -10821,7 +10829,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.5,
     colorByFamily: "#D3D3D3",
     color: "hsl(268.9, 100%, 69%)",
-    mass: 146.2
+    mass: 128.12922
   },
   G: {
     value: "G",
@@ -10830,7 +10838,7 @@ const proteinAlphabet = {
     hydrophobicity: -0.4,
     colorByFamily: "#00FFFF",
     color: "hsl(303.1, 100%, 69%)",
-    mass: 75.1
+    mass: 57.05132
   },
   H: {
     value: "H",
@@ -10839,7 +10847,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.2,
     colorByFamily: "#FFC0CB",
     color: "hsl(272.2, 100%, 69%)",
-    mass: 155.2
+    mass: 137.13928
   },
   I: {
     value: "I",
@@ -10848,7 +10856,7 @@ const proteinAlphabet = {
     hydrophobicity: 4.5,
     colorByFamily: "#00FFFF",
     color: "hsl(356.9, 100%, 69%)",
-    mass: 131.2
+    mass: 113.15764
   },
   L: {
     value: "L",
@@ -10857,7 +10865,7 @@ const proteinAlphabet = {
     hydrophobicity: 3.8,
     colorByFamily: "#00FFFF",
     color: "hsl(349.4, 100%, 69%)",
-    mass: 131.2
+    mass: 113.15764
   },
   K: {
     value: "K",
@@ -10866,7 +10874,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.9,
     colorByFamily: "#FFC0CB",
     color: "hsl(264.7, 100%, 69%)",
-    mass: 146.2
+    mass: 128.17228
   },
   M: {
     value: "M",
@@ -10875,7 +10883,7 @@ const proteinAlphabet = {
     hydrophobicity: 1.9,
     colorByFamily: "#FFFF00",
     color: "hsl(328.5, 100%, 69%)",
-    mass: 149.2
+    mass: 131.19606
   },
   F: {
     value: "F",
@@ -10884,7 +10892,7 @@ const proteinAlphabet = {
     hydrophobicity: 2.8,
     colorByFamily: "#FFA500",
     color: "hsl(338.4, 100%, 69%)",
-    mass: 165.2
+    mass: 147.17386
   },
   P: {
     value: "P",
@@ -10893,7 +10901,7 @@ const proteinAlphabet = {
     hydrophobicity: -1.6,
     colorByFamily: "#00FFFF",
     color: "hsl(289.9, 100%, 69%)",
-    mass: 115.1
+    mass: 97.11518
   },
   S: {
     value: "S",
@@ -10902,7 +10910,7 @@ const proteinAlphabet = {
     hydrophobicity: -0.8,
     colorByFamily: "#90EE90",
     color: "hsl(298.6, 100%, 69%)",
-    mass: 105.1
+    mass: 87.0773
   },
   T: {
     value: "T",
@@ -10911,7 +10919,7 @@ const proteinAlphabet = {
     hydrophobicity: -0.7,
     colorByFamily: "#90EE90",
     color: "hsl(299.8, 100%, 69%)",
-    mass: 119.1
+    mass: 101.10388
   },
   U: {
     value: "U",
@@ -10919,7 +10927,7 @@ const proteinAlphabet = {
     threeLettersName: "Sec",
     colorByFamily: "#FF0000",
     color: "hsl(0, 100%, 69%)",
-    mass: 168.1
+    mass: 150.3079
   },
   W: {
     value: "W",
@@ -10928,7 +10936,7 @@ const proteinAlphabet = {
     hydrophobicity: -0.9,
     colorByFamily: "#FFA500",
     color: "hsl(297.6, 100%, 69%)",
-    mass: 204.2
+    mass: 186.2099
   },
   Y: {
     value: "Y",
@@ -10937,7 +10945,7 @@ const proteinAlphabet = {
     hydrophobicity: -1.3,
     colorByFamily: "#FFA500",
     color: "hsl(293.2, 100%, 69%)",
-    mass: 181.2
+    mass: 163.17326
   },
   V: {
     value: "V",
@@ -10946,7 +10954,7 @@ const proteinAlphabet = {
     hydrophobicity: 4.2,
     colorByFamily: "#00FFFF",
     color: "hsl(353.6, 100%, 69%)",
-    mass: 117.1
+    mass: 99.13106
   },
   "*": {
     value: "*",
@@ -11391,13 +11399,13 @@ function coerceLocation({
     messages.push(
       "Invalid annotation start: " + location.start + " detected for " + location.name + " and set to size: " + size
     );
-    location.start = size - (isProtein ? 3 : 1);
+    location.start = Math.max(0, size - (isProtein ? 3 : 1));
   }
   if (location.end < 0 || !(location.end <= size - 1) || location.end > size - 1) {
     messages.push(
       "Invalid annotation end:  " + location.end + " detected for " + location.name + " and set to seq size: " + size
     );
-    location.end = size - 1;
+    location.end = Math.max(0, size - 1);
   }
   if (location.start > location.end && circular === false) {
     messages.push(
@@ -11410,9 +11418,9 @@ __name(coerceLocation, "coerceLocation");
 function filterAminoAcidSequenceString(sequenceString, options) {
   options = options || {};
   if (options.includeStopCodon) {
-    return sequenceString.replace(/[^xtgalmfwkqespvicyhrndu.*]/gi, "");
+    return sequenceString == null ? void 0 : sequenceString.replace(/[^xtgalmfwkqespvicyhrndu.*]/gi, "");
   }
-  return sequenceString.replace(/[^xtgalmfwkqespvicyhrndu]/gi, "");
+  return sequenceString == null ? void 0 : sequenceString.replace(/[^xtgalmfwkqespvicyhrndu]/gi, "");
 }
 __name(filterAminoAcidSequenceString, "filterAminoAcidSequenceString");
 function getDegenerateDnaStringFromAAString(aaString) {
@@ -11610,7 +11618,7 @@ const calcTmMethods = {
   calculateTemperature: function(sequence, type, A, R, C, Na) {
     if (typeof type === "undefined") {
       type = this.TABLE_BRESLAUER;
-    } else if (type != this.TABLE_BRESLAUER && (type != this.TABLE_UNIFIED && type != this.TABLE_SUGIMOTO)) {
+    } else if (type != this.TABLE_BRESLAUER && type != this.TABLE_UNIFIED && type != this.TABLE_SUGIMOTO) {
       throw new Error("Invalid table type!");
     }
     if (!A) {
@@ -19761,18 +19769,20 @@ function genbankToJson(string, options = {}) {
       const isKeyRunon = isKeywordRunon(line);
       const isSubKey = isSubKeyword(line);
       const isKey = isKeyword(line);
-      if (key === "LOCUS") {
-        LINETYPE = key;
-      } else if (key === "REFERENCE") {
-        LINETYPE = key;
-      } else if (key === "FEATURES") {
-        LINETYPE = key;
-      } else if (key === "ORIGIN") {
-        LINETYPE = key;
-      } else if (key === "//") {
-        LINETYPE = key;
-      } else if (isKey === true) {
-        LINETYPE = key;
+      if (!isKeyRunon) {
+        if (key === "LOCUS") {
+          LINETYPE = key;
+        } else if (key === "REFERENCE") {
+          LINETYPE = key;
+        } else if (key === "FEATURES") {
+          LINETYPE = key;
+        } else if (key === "ORIGIN") {
+          LINETYPE = key;
+        } else if (key === "//") {
+          LINETYPE = key;
+        } else if (isKey === true) {
+          LINETYPE = key;
+        }
       }
       if (line.trim() === "" || key === ";") {
         return false;
@@ -19941,7 +19951,6 @@ function genbankToJson(string, options = {}) {
   __name(parseOrigin, "parseOrigin");
   function parseLocus(line) {
     result = createInitialSequence(options);
-    let locusName;
     let circular;
     let gbDivision;
     let date;
@@ -19952,7 +19961,7 @@ function genbankToJson(string, options = {}) {
       );
       addMessage("Import Warning: Locus line contains no values: " + line);
     }
-    locusName = lineArr[1];
+    const locusName = lineArr[1];
     for (let i = 1; i < lineArr.length; i++) {
       if (lineArr[i].match(/circular/gi)) {
         circular = true;
@@ -20105,10 +20114,10 @@ function genbankToJson(string, options = {}) {
   }
   __name(parseFeatureLocation, "parseFeatureLocation");
   function parseFeatureNote(line) {
-    let newLine, lineArr;
+    let newLine;
     newLine = line.trimLeft();
     newLine = newLine.replace(/^\/|"$/g, "");
-    lineArr = newLine.split(/="|=/);
+    const lineArr = newLine.split(/="|=/);
     let val2 = lineArr.slice(1).join("=");
     if (val2) {
       val2 = val2.replace(/\\/g, " ");
@@ -29914,13 +29923,10 @@ function geneiousXmlToJson(string, options) {
           });
         }
       });
-      const toRet = lodashExports.filter(
-        resultArray,
-        (r) => {
-          var _a3, _b3;
-          return (_b3 = (_a3 = r == null ? void 0 : r.parsedSequence) == null ? void 0 : _a3.sequence) == null ? void 0 : _b3.length;
-        }
-      );
+      const toRet = lodashExports.filter(resultArray, (r) => {
+        var _a3, _b3;
+        return (_b3 = (_a3 = r == null ? void 0 : r.parsedSequence) == null ? void 0 : _a3.sequence) == null ? void 0 : _b3.length;
+      });
       if (toRet.length)
         return toRet;
       return onFileParsed(resultArray);
@@ -30025,13 +30031,10 @@ function jbeiXmlToJson(string, options) {
           messages: ["Error while parsing JBEI format"]
         });
       }
-      const toRet = lodashExports.filter(
-        resultArray,
-        (r) => {
-          var _a3, _b3;
-          return (_b3 = (_a3 = r == null ? void 0 : r.parsedSequence) == null ? void 0 : _a3.sequence) == null ? void 0 : _b3.length;
-        }
-      );
+      const toRet = lodashExports.filter(resultArray, (r) => {
+        var _a3, _b3;
+        return (_b3 = (_a3 = r == null ? void 0 : r.parsedSequence) == null ? void 0 : _a3.sequence) == null ? void 0 : _b3.length;
+      });
       if (toRet.length)
         return toRet;
       return onFileParsed(resultArray);
@@ -32415,7 +32418,6 @@ function createGenbankLocus(serSeq, options) {
   if (serSeq.sequence.symbols) {
     serSeq.sequence = serSeq.sequence.symbols.split("");
   }
-  let tmp;
   let dnaType;
   if (serSeq.isProtein) {
     dnaType = "";
@@ -32432,7 +32434,7 @@ function createGenbankLocus(serSeq, options) {
   line += " ";
   line += StringUtil.lpad(String(serSeq.sequence.length), " ", 11);
   line += serSeq.isProtein ? " aa " : " bp ";
-  tmp = "";
+  const tmp = "";
   line += StringUtil.lpad(tmp, " ", 3);
   line += StringUtil.rpad(dnaType, " ", 6);
   line += "  ";