@teselagen/bio-parsers 0.4.34 → 0.4.36

package/index.cjs

@@ -12866,6 +12866,10 @@ function genbankToJson(string, options = {}) {
       feat.name = feat.notes.ApEinfo_label[0];
     } else if (feat.notes.name) {
       feat.name = feat.notes.name[0];
+    } else if (feat.notes.product) {
+      feat.name = feat.notes.product[0];
+    } else if (feat.notes.region_name) {
+      feat.name = feat.notes.region_name[0];
     } else if (feat.notes.organism) {
       feat.name = feat.notes.organism[0];
     } else if (feat.notes.locus_tag) {
@@ -23817,7 +23821,44 @@ 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

@@ -12864,6 +12864,10 @@ function genbankToJson(string, options = {}) {
       feat.name = feat.notes.ApEinfo_label[0];
     } else if (feat.notes.name) {
       feat.name = feat.notes.name[0];
+    } else if (feat.notes.product) {
+      feat.name = feat.notes.product[0];
+    } else if (feat.notes.region_name) {
+      feat.name = feat.notes.region_name[0];
     } else if (feat.notes.organism) {
       feat.name = feat.notes.organism[0];
     } else if (feat.notes.locus_tag) {
@@ -23815,7 +23819,44 @@ 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

@@ -12868,6 +12868,10 @@ var __async = (__this, __arguments, generator) => {
         feat.name = feat.notes.ApEinfo_label[0];
       } else if (feat.notes.name) {
         feat.name = feat.notes.name[0];
+      } else if (feat.notes.product) {
+        feat.name = feat.notes.product[0];
+      } else if (feat.notes.region_name) {
+        feat.name = feat.notes.region_name[0];
       } else if (feat.notes.organism) {
         feat.name = feat.notes.organism[0];
       } else if (feat.notes.locus_tag) {
@@ -23819,7 +23823,44 @@ ${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": "0.4.34",
+  "version": "0.4.36",
   "type": "module",
   "repository": "https://github.com/TeselaGen/tg-oss",
   "dependencies": {

package/src/genbankToJson.js

@@ -708,6 +708,10 @@ function genbankToJson(string, options = {}) {
       feat.name = feat.notes.ApEinfo_label[0];
     } else if (feat.notes.name) {
       feat.name = feat.notes.name[0];
+    } else if (feat.notes.product) {
+      feat.name = feat.notes.product[0];
+    } else if (feat.notes.region_name) {
+      feat.name = feat.notes.region_name[0];
     } else if (feat.notes.organism) {
       feat.name = feat.notes.organism[0];
     } else if (feat.notes.locus_tag) {

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 +