@teselagen/bio-parsers 0.4.36 → 0.4.38

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) {
@@ -23674,6 +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;
@@ -23868,33 +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

@@ -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) {
@@ -23672,6 +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;
@@ -23866,33 +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

@@ -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) {
@@ -23676,6 +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;
@@ -23870,33 +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": "0.4.36",
+  "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);
 

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) {