@teselagen/bio-parsers 0.4.37 → 0.4.38

package/index.cjs

@@ -23681,6 +23681,38 @@ function cutUpStr(val2, start, end) {
   return val2.slice(start, end);
 }
 __name(cutUpStr, "cutUpStr");
+function featureToGenbankLocationString(feat, options) {
+  const { inclusive1BasedStart, inclusive1BasedEnd, isProtein } = options;
+  let locStr = "";
+  if (feat.locations && feat.locations.length > 1) {
+    feat.locations.forEach((loc, i) => {
+      locStr += getProteinStart(
+        parseInt(loc.start, 10) + (inclusive1BasedStart ? 0 : 1),
+        isProtein
+      ) + ".." + getProteinEnd(
+        parseInt(loc.end, 10) + (inclusive1BasedEnd ? 0 : 1),
+        isProtein
+      );
+      if (i !== feat.locations.length - 1) {
+        locStr += ",";
+      }
+    });
+    locStr = "join(" + locStr + ")";
+  } else {
+    locStr += getProteinStart(
+      parseInt(feat.start, 10) + (inclusive1BasedStart ? 0 : 1),
+      isProtein
+    ) + ".." + getProteinEnd(
+      parseInt(feat.end, 10) + (inclusive1BasedEnd ? 0 : 1),
+      isProtein
+    );
+  }
+  if (feat.strand === -1) {
+    locStr = "complement(" + locStr + ")";
+  }
+  return locStr;
+}
+__name(featureToGenbankLocationString, "featureToGenbankLocationString");
 function jsonToGenbank(_serSeq, options) {
   options = options || {};
   options.reformatSeqName = options.reformatSeqName !== false;
@@ -23875,33 +23907,7 @@ function featureToGenbankString(feat, options) {
     feat.type = "primer_bind";
   }
   const line = "     " + StringUtil.rpad(feat.type || "misc_feature", " ", options.featurePadLength);
-  let locStr = "";
-  if (feat.locations && feat.locations.length > 1) {
-    feat.locations.forEach((loc, i) => {
-      locStr += getProteinStart(
-        parseInt(loc.start, 10) + (options.inclusive1BasedStart ? 0 : 1),
-        options.isProtein
-      ) + ".." + getProteinEnd(
-        parseInt(loc.end, 10) + (options.inclusive1BasedEnd ? 0 : 1),
-        options.isProtein
-      );
-      if (i !== feat.locations.length - 1) {
-        locStr += ",";
-      }
-    });
-    locStr = "join(" + locStr + ")";
-  } else {
-    locStr += getProteinStart(
-      parseInt(feat.start, 10) + (options.inclusive1BasedStart ? 0 : 1),
-      options.isProtein
-    ) + ".." + getProteinEnd(
-      parseInt(feat.end, 10) + (options.inclusive1BasedEnd ? 0 : 1),
-      options.isProtein
-    );
-  }
-  if (feat.strand === -1) {
-    locStr = "complement(" + locStr + ")";
-  }
+  const locStr = featureToGenbankLocationString(feat, options);
   lines.push(line + locStr);
   lines.push(
     featureNoteInDataToGenbankString(

package/index.js

@@ -23679,6 +23679,38 @@ function cutUpStr(val2, start, end) {
   return val2.slice(start, end);
 }
 __name(cutUpStr, "cutUpStr");
+function featureToGenbankLocationString(feat, options) {
+  const { inclusive1BasedStart, inclusive1BasedEnd, isProtein } = options;
+  let locStr = "";
+  if (feat.locations && feat.locations.length > 1) {
+    feat.locations.forEach((loc, i) => {
+      locStr += getProteinStart(
+        parseInt(loc.start, 10) + (inclusive1BasedStart ? 0 : 1),
+        isProtein
+      ) + ".." + getProteinEnd(
+        parseInt(loc.end, 10) + (inclusive1BasedEnd ? 0 : 1),
+        isProtein
+      );
+      if (i !== feat.locations.length - 1) {
+        locStr += ",";
+      }
+    });
+    locStr = "join(" + locStr + ")";
+  } else {
+    locStr += getProteinStart(
+      parseInt(feat.start, 10) + (inclusive1BasedStart ? 0 : 1),
+      isProtein
+    ) + ".." + getProteinEnd(
+      parseInt(feat.end, 10) + (inclusive1BasedEnd ? 0 : 1),
+      isProtein
+    );
+  }
+  if (feat.strand === -1) {
+    locStr = "complement(" + locStr + ")";
+  }
+  return locStr;
+}
+__name(featureToGenbankLocationString, "featureToGenbankLocationString");
 function jsonToGenbank(_serSeq, options) {
   options = options || {};
   options.reformatSeqName = options.reformatSeqName !== false;
@@ -23873,33 +23905,7 @@ function featureToGenbankString(feat, options) {
     feat.type = "primer_bind";
   }
   const line = "     " + StringUtil.rpad(feat.type || "misc_feature", " ", options.featurePadLength);
-  let locStr = "";
-  if (feat.locations && feat.locations.length > 1) {
-    feat.locations.forEach((loc, i) => {
-      locStr += getProteinStart(
-        parseInt(loc.start, 10) + (options.inclusive1BasedStart ? 0 : 1),
-        options.isProtein
-      ) + ".." + getProteinEnd(
-        parseInt(loc.end, 10) + (options.inclusive1BasedEnd ? 0 : 1),
-        options.isProtein
-      );
-      if (i !== feat.locations.length - 1) {
-        locStr += ",";
-      }
-    });
-    locStr = "join(" + locStr + ")";
-  } else {
-    locStr += getProteinStart(
-      parseInt(feat.start, 10) + (options.inclusive1BasedStart ? 0 : 1),
-      options.isProtein
-    ) + ".." + getProteinEnd(
-      parseInt(feat.end, 10) + (options.inclusive1BasedEnd ? 0 : 1),
-      options.isProtein
-    );
-  }
-  if (feat.strand === -1) {
-    locStr = "complement(" + locStr + ")";
-  }
+  const locStr = featureToGenbankLocationString(feat, options);
   lines.push(line + locStr);
   lines.push(
     featureNoteInDataToGenbankString(

package/index.umd.cjs

@@ -23683,6 +23683,38 @@ ${seq.sequence}
     return val2.slice(start, end);
   }
   __name(cutUpStr, "cutUpStr");
+  function featureToGenbankLocationString(feat, options) {
+    const { inclusive1BasedStart, inclusive1BasedEnd, isProtein } = options;
+    let locStr = "";
+    if (feat.locations && feat.locations.length > 1) {
+      feat.locations.forEach((loc, i2) => {
+        locStr += getProteinStart(
+          parseInt(loc.start, 10) + (inclusive1BasedStart ? 0 : 1),
+          isProtein
+        ) + ".." + getProteinEnd(
+          parseInt(loc.end, 10) + (inclusive1BasedEnd ? 0 : 1),
+          isProtein
+        );
+        if (i2 !== feat.locations.length - 1) {
+          locStr += ",";
+        }
+      });
+      locStr = "join(" + locStr + ")";
+    } else {
+      locStr += getProteinStart(
+        parseInt(feat.start, 10) + (inclusive1BasedStart ? 0 : 1),
+        isProtein
+      ) + ".." + getProteinEnd(
+        parseInt(feat.end, 10) + (inclusive1BasedEnd ? 0 : 1),
+        isProtein
+      );
+    }
+    if (feat.strand === -1) {
+      locStr = "complement(" + locStr + ")";
+    }
+    return locStr;
+  }
+  __name(featureToGenbankLocationString, "featureToGenbankLocationString");
   function jsonToGenbank(_serSeq, options) {
     options = options || {};
     options.reformatSeqName = options.reformatSeqName !== false;
@@ -23877,33 +23909,7 @@ ${seq.sequence}
       feat.type = "primer_bind";
     }
     const line = "     " + StringUtil.rpad(feat.type || "misc_feature", " ", options.featurePadLength);
-    let locStr = "";
-    if (feat.locations && feat.locations.length > 1) {
-      feat.locations.forEach((loc, i2) => {
-        locStr += getProteinStart(
-          parseInt(loc.start, 10) + (options.inclusive1BasedStart ? 0 : 1),
-          options.isProtein
-        ) + ".." + getProteinEnd(
-          parseInt(loc.end, 10) + (options.inclusive1BasedEnd ? 0 : 1),
-          options.isProtein
-        );
-        if (i2 !== feat.locations.length - 1) {
-          locStr += ",";
-        }
-      });
-      locStr = "join(" + locStr + ")";
-    } else {
-      locStr += getProteinStart(
-        parseInt(feat.start, 10) + (options.inclusive1BasedStart ? 0 : 1),
-        options.isProtein
-      ) + ".." + getProteinEnd(
-        parseInt(feat.end, 10) + (options.inclusive1BasedEnd ? 0 : 1),
-        options.isProtein
-      );
-    }
-    if (feat.strand === -1) {
-      locStr = "complement(" + locStr + ")";
-    }
+    const locStr = featureToGenbankLocationString(feat, options);
     lines.push(line + locStr);
     lines.push(
       featureNoteInDataToGenbankString(

package/jsonToGenbank.d.ts

@@ -1 +1,2 @@
+export function featureToGenbankLocationString(feat: any, options: any): string;
 export default function _default(_serSeq: any, options: any): string | false;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.37",
+  "version": "0.4.38",
   "type": "module",
   "repository": "https://github.com/TeselaGen/tg-oss",
   "dependencies": {

package/src/jsonToGenbank.js

@@ -76,6 +76,47 @@ function cutUpStr(val, start, end) {
   return val.slice(start, end);
 }
 
+export function featureToGenbankLocationString(feat, options) {
+  const { inclusive1BasedStart, inclusive1BasedEnd, isProtein } = options;
+  let locStr = "";
+
+  if (feat.locations && feat.locations.length > 1) {
+    feat.locations.forEach((loc, i) => {
+      locStr +=
+        getProteinStart(
+          parseInt(loc.start, 10) + (inclusive1BasedStart ? 0 : 1),
+          isProtein
+        ) +
+        ".." +
+        getProteinEnd(
+          parseInt(loc.end, 10) + (inclusive1BasedEnd ? 0 : 1),
+          isProtein
+        );
+
+      if (i !== feat.locations.length - 1) {
+        locStr += ",";
+      }
+    });
+    locStr = "join(" + locStr + ")";
+  } else {
+    locStr +=
+      getProteinStart(
+        parseInt(feat.start, 10) + (inclusive1BasedStart ? 0 : 1),
+        isProtein
+      ) +
+      ".." +
+      getProteinEnd(
+        parseInt(feat.end, 10) + (inclusive1BasedEnd ? 0 : 1),
+        isProtein
+      );
+  }
+
+  if (feat.strand === -1) {
+    locStr = "complement(" + locStr + ")";
+  }
+  return locStr;
+}
+
 export default function (_serSeq, options) {
   options = options || {};
   options.reformatSeqName = options.reformatSeqName !== false;
@@ -325,49 +366,8 @@ function featureToGenbankString(feat, options) {
   const line =
     "     " +
     StringUtil.rpad(feat.type || "misc_feature", " ", options.featurePadLength);
-  let locStr = "";
-
-  //for(var i=0;i<feat.locations.length;i++) {
-  //	var loc = feat.locations[i];
-  //	locStr.push((loc.start+1) + '..' + loc.end);
-  //}
 
-  if (feat.locations && feat.locations.length > 1) {
-    feat.locations.forEach((loc, i) => {
-      locStr +=
-        getProteinStart(
-          parseInt(loc.start, 10) + (options.inclusive1BasedStart ? 0 : 1),
-          options.isProtein
-        ) +
-        ".." +
-        getProteinEnd(
-          parseInt(loc.end, 10) + (options.inclusive1BasedEnd ? 0 : 1),
-          options.isProtein
-        );
-
-      if (i !== feat.locations.length - 1) {
-        locStr += ",";
-      }
-    });
-    locStr = "join(" + locStr + ")";
-  } else {
-    locStr +=
-      getProteinStart(
-        parseInt(feat.start, 10) + (options.inclusive1BasedStart ? 0 : 1),
-        options.isProtein
-      ) +
-      ".." +
-      getProteinEnd(
-        parseInt(feat.end, 10) + (options.inclusive1BasedEnd ? 0 : 1),
-        options.isProtein
-      );
-  }
-
-  // locStr = locStr.join(",");
-
-  if (feat.strand === -1) {
-    locStr = "complement(" + locStr + ")";
-  }
+  const locStr = featureToGenbankLocationString(feat, options);
 
   lines.push(line + locStr);