@teselagen/bio-parsers 0.4.35 → 0.4.37

package/index.cjs

@@ -17145,17 +17145,20 @@ function snapgeneToJson(_0) {
           const b = new fxpExports.XMLParser({
             ignoreAttributes: false,
             attributeNamePrefix: "",
-            isArray: /* @__PURE__ */ __name((name) => name === "Feature" || name === "Segment", "isArray")
+            isArray: /* @__PURE__ */ __name((name) => ["Feature", "Segment", "Q", "V"].includes(name), "isArray")
           }).parse(xml);
           const { Features: { Feature = [] } = {} } = b;
           data.features = [];
           Feature.forEach((feat) => {
+            var _a2, _b2, _c, _d;
             const { directionality, Segment = [], name, type } = feat;
+            let color2;
             let maxStart = 0;
             let maxEnd = 0;
             const locations = Segment && Segment.map((seg) => {
               if (!seg) throw new Error("invalid feature definition");
               const { range } = seg;
+              if (seg.color) color2 = seg.color;
               let { start, end } = getStartAndEndFromRangeString(range);
               start = isProtein ? start * 3 : start;
               end = isProtein ? end * 3 + 2 : end;
@@ -17166,6 +17169,10 @@ function snapgeneToJson(_0) {
                 end
               };
             });
+            const colorQual = (_a2 = feat.Q) == null ? void 0 : _a2.find((q) => q.name === "color");
+            if (colorQual) {
+              color2 = ((_c = (_b2 = colorQual.V) == null ? void 0 : _b2[0]) == null ? void 0 : _c.text) || ((_d = colorQual.V) == null ? void 0 : _d[0]);
+            }
             data.features.push(__spreadProps(__spreadValues({
               name,
               type
@@ -17173,8 +17180,8 @@ function snapgeneToJson(_0) {
               strand: directionality ? strand_dict[directionality][0] : 1,
               arrowheadType: directionality ? strand_dict[directionality][1] : "NONE",
               start: maxStart,
-              end: maxEnd
-              // color,
+              end: maxEnd,
+              color: color2
             }));
           });
         } else if (ord(next_byte) === 6) {
@@ -23821,7 +23828,44 @@ function getCurrentDateString() {
   return day + "-" + month + "-" + year;
 }
 __name(getCurrentDateString, "getCurrentDateString");
+const standardLineLength = 79;
 function featureNoteInDataToGenbankString(name, value, options) {
+  const valueString = mangleOrStripUrls(value, options);
+  if (valueString.length > standardLineLength - 25 - name.length) {
+    const lines = [];
+    let currentIndex = 0;
+    while (currentIndex < valueString.length) {
+      if (currentIndex === 0) {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - name.length - 24
+        );
+        lines.push(
+          StringUtil.lpad("/", " ", 22) + name + '="' + chunk + (currentIndex + standardLineLength - 22 - name.length >= valueString.length ? '"' : "")
+        );
+        currentIndex += standardLineLength - name.length - 24;
+      } else {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - 21
+        );
+        if (currentIndex + standardLineLength - 21 >= valueString.length) {
+          const lineString = " ".repeat(21) + chunk;
+          if (lineString.length === standardLineLength) {
+            lines.push(lineString);
+            lines.push(" ".repeat(21) + '"');
+          } else {
+            lines.push(lineString + '"');
+          }
+        } else {
+          const lineString = " ".repeat(21) + chunk;
+          lines.push(lineString);
+        }
+        currentIndex += standardLineLength - 21;
+      }
+    }
+    return lines.join("\r\n");
+  }
   return StringUtil.lpad("/", " ", 22) + name + '="' + mangleOrStripUrls(value, options) + '"';
 }
 __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");

package/index.js

@@ -17143,17 +17143,20 @@ function snapgeneToJson(_0) {
           const b = new fxpExports.XMLParser({
             ignoreAttributes: false,
             attributeNamePrefix: "",
-            isArray: /* @__PURE__ */ __name((name) => name === "Feature" || name === "Segment", "isArray")
+            isArray: /* @__PURE__ */ __name((name) => ["Feature", "Segment", "Q", "V"].includes(name), "isArray")
           }).parse(xml);
           const { Features: { Feature = [] } = {} } = b;
           data.features = [];
           Feature.forEach((feat) => {
+            var _a2, _b2, _c, _d;
             const { directionality, Segment = [], name, type } = feat;
+            let color2;
             let maxStart = 0;
             let maxEnd = 0;
             const locations = Segment && Segment.map((seg) => {
               if (!seg) throw new Error("invalid feature definition");
               const { range } = seg;
+              if (seg.color) color2 = seg.color;
               let { start, end } = getStartAndEndFromRangeString(range);
               start = isProtein ? start * 3 : start;
               end = isProtein ? end * 3 + 2 : end;
@@ -17164,6 +17167,10 @@ function snapgeneToJson(_0) {
                 end
               };
             });
+            const colorQual = (_a2 = feat.Q) == null ? void 0 : _a2.find((q) => q.name === "color");
+            if (colorQual) {
+              color2 = ((_c = (_b2 = colorQual.V) == null ? void 0 : _b2[0]) == null ? void 0 : _c.text) || ((_d = colorQual.V) == null ? void 0 : _d[0]);
+            }
             data.features.push(__spreadProps(__spreadValues({
               name,
               type
@@ -17171,8 +17178,8 @@ function snapgeneToJson(_0) {
               strand: directionality ? strand_dict[directionality][0] : 1,
               arrowheadType: directionality ? strand_dict[directionality][1] : "NONE",
               start: maxStart,
-              end: maxEnd
-              // color,
+              end: maxEnd,
+              color: color2
             }));
           });
         } else if (ord(next_byte) === 6) {
@@ -23819,7 +23826,44 @@ function getCurrentDateString() {
   return day + "-" + month + "-" + year;
 }
 __name(getCurrentDateString, "getCurrentDateString");
+const standardLineLength = 79;
 function featureNoteInDataToGenbankString(name, value, options) {
+  const valueString = mangleOrStripUrls(value, options);
+  if (valueString.length > standardLineLength - 25 - name.length) {
+    const lines = [];
+    let currentIndex = 0;
+    while (currentIndex < valueString.length) {
+      if (currentIndex === 0) {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - name.length - 24
+        );
+        lines.push(
+          StringUtil.lpad("/", " ", 22) + name + '="' + chunk + (currentIndex + standardLineLength - 22 - name.length >= valueString.length ? '"' : "")
+        );
+        currentIndex += standardLineLength - name.length - 24;
+      } else {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - 21
+        );
+        if (currentIndex + standardLineLength - 21 >= valueString.length) {
+          const lineString = " ".repeat(21) + chunk;
+          if (lineString.length === standardLineLength) {
+            lines.push(lineString);
+            lines.push(" ".repeat(21) + '"');
+          } else {
+            lines.push(lineString + '"');
+          }
+        } else {
+          const lineString = " ".repeat(21) + chunk;
+          lines.push(lineString);
+        }
+        currentIndex += standardLineLength - 21;
+      }
+    }
+    return lines.join("\r\n");
+  }
   return StringUtil.lpad("/", " ", 22) + name + '="' + mangleOrStripUrls(value, options) + '"';
 }
 __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");

package/index.umd.cjs

@@ -17147,17 +17147,20 @@ var __async = (__this, __arguments, generator) => {
             const b = new fxpExports.XMLParser({
               ignoreAttributes: false,
               attributeNamePrefix: "",
-              isArray: /* @__PURE__ */ __name((name) => name === "Feature" || name === "Segment", "isArray")
+              isArray: /* @__PURE__ */ __name((name) => ["Feature", "Segment", "Q", "V"].includes(name), "isArray")
             }).parse(xml);
             const { Features: { Feature = [] } = {} } = b;
             data.features = [];
             Feature.forEach((feat) => {
+              var _a2, _b2, _c, _d;
               const { directionality, Segment = [], name, type } = feat;
+              let color2;
               let maxStart = 0;
               let maxEnd = 0;
               const locations = Segment && Segment.map((seg) => {
                 if (!seg) throw new Error("invalid feature definition");
                 const { range } = seg;
+                if (seg.color) color2 = seg.color;
                 let { start, end } = getStartAndEndFromRangeString(range);
                 start = isProtein ? start * 3 : start;
                 end = isProtein ? end * 3 + 2 : end;
@@ -17168,6 +17171,10 @@ var __async = (__this, __arguments, generator) => {
                   end
                 };
               });
+              const colorQual = (_a2 = feat.Q) == null ? void 0 : _a2.find((q) => q.name === "color");
+              if (colorQual) {
+                color2 = ((_c = (_b2 = colorQual.V) == null ? void 0 : _b2[0]) == null ? void 0 : _c.text) || ((_d = colorQual.V) == null ? void 0 : _d[0]);
+              }
               data.features.push(__spreadProps(__spreadValues({
                 name,
                 type
@@ -17175,8 +17182,8 @@ var __async = (__this, __arguments, generator) => {
                 strand: directionality ? strand_dict[directionality][0] : 1,
                 arrowheadType: directionality ? strand_dict[directionality][1] : "NONE",
                 start: maxStart,
-                end: maxEnd
-                // color,
+                end: maxEnd,
+                color: color2
               }));
             });
           } else if (ord(next_byte) === 6) {
@@ -23823,7 +23830,44 @@ ${seq.sequence}
     return day + "-" + month + "-" + year;
   }
   __name(getCurrentDateString, "getCurrentDateString");
+  const standardLineLength = 79;
   function featureNoteInDataToGenbankString(name, value, options) {
+    const valueString = mangleOrStripUrls(value, options);
+    if (valueString.length > standardLineLength - 25 - name.length) {
+      const lines = [];
+      let currentIndex = 0;
+      while (currentIndex < valueString.length) {
+        if (currentIndex === 0) {
+          const chunk = valueString.substring(
+            currentIndex,
+            currentIndex + standardLineLength - name.length - 24
+          );
+          lines.push(
+            StringUtil.lpad("/", " ", 22) + name + '="' + chunk + (currentIndex + standardLineLength - 22 - name.length >= valueString.length ? '"' : "")
+          );
+          currentIndex += standardLineLength - name.length - 24;
+        } else {
+          const chunk = valueString.substring(
+            currentIndex,
+            currentIndex + standardLineLength - 21
+          );
+          if (currentIndex + standardLineLength - 21 >= valueString.length) {
+            const lineString = " ".repeat(21) + chunk;
+            if (lineString.length === standardLineLength) {
+              lines.push(lineString);
+              lines.push(" ".repeat(21) + '"');
+            } else {
+              lines.push(lineString + '"');
+            }
+          } else {
+            const lineString = " ".repeat(21) + chunk;
+            lines.push(lineString);
+          }
+          currentIndex += standardLineLength - 21;
+        }
+      }
+      return lines.join("\r\n");
+    }
     return StringUtil.lpad("/", " ", 22) + name + '="' + mangleOrStripUrls(value, options) + '"';
   }
   __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.35",
+  "version": "0.4.37",
   "type": "module",
   "repository": "https://github.com/TeselaGen/tg-oss",
   "dependencies": {

package/src/jsonToGenbank.js

@@ -6,6 +6,7 @@ import pragmasAndTypes from "./utils/pragmasAndTypes.js";
 import { mangleOrStripUrls } from "./utils/unmangleUrls.js";
 import { reformatName } from "./utils/NameUtils.js";
 import { getFeatureToColorMap } from "@teselagen/sequence-utils";
+
 const StringUtil = {
   /** Trims white space at beginning and end of string
    * @param {string} line
@@ -206,11 +207,11 @@ function createGenbankLocus(serSeq, options) {
   } else if (serSeq.type === "RNA") {
     dnaType = serSeq?.doubleStranded
       ? "RNA"
-      : serSeq?.sequenceTypeFromLocus ?? "ss-RNA";
+      : (serSeq?.sequenceTypeFromLocus ?? "ss-RNA");
   } else {
     dnaType = serSeq?.doubleStranded
       ? "DNA"
-      : serSeq?.sequenceTypeFromLocus ?? "DNA";
+      : (serSeq?.sequenceTypeFromLocus ?? "DNA");
   }
   const date = getCurrentDateString();
 
@@ -257,7 +258,56 @@ function getCurrentDateString() {
   return day + "-" + month + "-" + year;
 }
 
+const standardLineLength = 79;
 function featureNoteInDataToGenbankString(name, value, options) {
+  const valueString = mangleOrStripUrls(value, options);
+  // if valueString.length is larger than standardLineLength - 25 - name.length,
+  // we need to split it up into multiple lines, to make sure each line has 21 spaces
+  // a maximum of 59 additional characters
+  // 25 is the length of '/', '=', two '"' and the 21 spaces.
+  if (valueString.length > standardLineLength - 25 - name.length) {
+    const lines = [];
+    let currentIndex = 0;
+    while (currentIndex < valueString.length) {
+      if (currentIndex === 0) {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - name.length - 24
+        );
+        lines.push(
+          StringUtil.lpad("/", " ", 22) +
+            name +
+            '="' +
+            chunk +
+            (currentIndex + standardLineLength - 22 - name.length >=
+            valueString.length
+              ? '"'
+              : "")
+        );
+        currentIndex += standardLineLength - name.length - 24;
+      } else {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - 21
+        );
+        if (currentIndex + standardLineLength - 21 >= valueString.length) {
+          const lineString = " ".repeat(21) + chunk;
+          if (lineString.length === standardLineLength) {
+            lines.push(lineString);
+            lines.push(" ".repeat(21) + '"');
+          } else {
+            lines.push(lineString + '"');
+          }
+        } else {
+          const lineString = " ".repeat(21) + chunk;
+          lines.push(lineString);
+        }
+        currentIndex += standardLineLength - 21;
+      }
+    }
+    return lines.join("\r\n");
+  }
+
   return (
     StringUtil.lpad("/", " ", 22) +
     name +

package/src/snapgeneToJson.js

@@ -113,13 +113,13 @@ async function snapgeneToJson(fileObj, options = {}) {
         const b = new XMLParser({
           ignoreAttributes: false,
           attributeNamePrefix: "",
-          isArray: name => name === "Feature" || name === "Segment"
+          isArray: name => ["Feature", "Segment", "Q", "V"].includes(name)
         }).parse(xml);
         const { Features: { Feature = [] } = {} } = b;
         data.features = [];
         Feature.forEach(feat => {
           const { directionality, Segment = [], name, type } = feat;
-          // let color;
+          let color;
           let maxStart = 0;
           let maxEnd = 0;
           const locations =
@@ -127,7 +127,7 @@ async function snapgeneToJson(fileObj, options = {}) {
             Segment.map(seg => {
               if (!seg) throw new Error("invalid feature definition");
               const { range } = seg;
-              // color = seg.color;
+              if (seg.color) color = seg.color;
               let { start, end } = getStartAndEndFromRangeString(range);
               start = isProtein ? start * 3 : start;
               end = isProtein ? end * 3 + 2 : end;
@@ -139,6 +139,11 @@ async function snapgeneToJson(fileObj, options = {}) {
               };
             });
 
+          const colorQual = feat.Q?.find(q => q.name === "color");
+          if (colorQual) {
+            color = colorQual.V?.[0]?.text || colorQual.V?.[0];
+          }
+
           data.features.push({
             name,
             type,
@@ -148,8 +153,8 @@ async function snapgeneToJson(fileObj, options = {}) {
               ? strand_dict[directionality][1]
               : "NONE",
             start: maxStart,
-            end: maxEnd
-            // color,
+            end: maxEnd,
+            color
           });
         });
       } else if (ord(next_byte) === 6) {