@teselagen/bio-parsers 0.4.3 → 0.4.5

package/genbankToJson.d.ts

@@ -1,2 +1,3 @@
+export function parseFeatureLocation(locStr: any, isProtein: any, inclusive1BasedStart: any, inclusive1BasedEnd: any): any[];
 export default genbankToJson;
 declare function genbankToJson(string: any, options?: {}): any;

package/index.d.ts

@@ -1,6 +1,5 @@
 export { default as anyToJson } from "./anyToJson";
 export { default as fastaToJson } from "./fastaToJson";
-export { default as genbankToJson } from "./genbankToJson";
 export { default as sbolXmlToJson } from "./sbolXmlToJson";
 export { default as geneiousXmlToJson } from "./geneiousXmlToJson";
 export { default as jbeiXmlToJson } from "./jbeiXmlToJson";
@@ -12,5 +11,6 @@ export { default as cleanUpTeselagenJsonForExport } from "./utils/cleanUpTeselag
 export { default as parseUracilFeatures } from "./utils/parseUracilFeatures";
 export { default as jsonToJsonString } from "./jsonToJsonString";
 export { default as validateSequenceArray } from "./utils/validateSequenceArray";
+export { default as genbankToJson, parseFeatureLocation } from "./genbankToJson";
 export { default as ab1ToJson, convertBasePosTraceToPerBpTrace } from "./ab1ToJson";
 export { default as searchWholeObjByName, searchWholeObjByNameSimple, searchWholeObjByNameSimpleArray } from "./utils/searchWholeObjByName";

package/index.js

@@ -19779,6 +19779,30 @@ function flattenSequenceArray(parsingResultArray, opts) {
   return parsingResultArray;
 }
 __name(flattenSequenceArray, "flattenSequenceArray");
+function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd) {
+  locStr = locStr.trim();
+  const locArr = [];
+  locStr.replace(/(\d+)/g, function(string, match) {
+    locArr.push(match);
+  });
+  const locArray = [];
+  for (let i = 0; i < locArr.length; i += 2) {
+    const start = parseInt(locArr[i], 10) - (inclusive1BasedStart ? 0 : 1);
+    let end = parseInt(locArr[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
+    if (isNaN(end)) {
+      end = start;
+    }
+    const location = {
+      start,
+      end
+    };
+    locArray.push(
+      isProtein ? convertAACaretPositionOrRangeToDna(location) : location
+    );
+  }
+  return locArray;
+}
+__name(parseFeatureLocation, "parseFeatureLocation");
 function genbankToJson(string, options = {}) {
   const {
     inclusive1BasedStart,
@@ -20103,7 +20127,15 @@ function genbankToJson(string, options = {}) {
     }
     if (isFeatureLineRunon(line, featureLocationIndentation)) {
       if (lastLineWasLocation) {
-        parseFeatureLocation(line.trim(), options);
+        const feat = getCurrentFeature();
+        feat.locations = feat.locations.concat(
+          parseFeatureLocation(
+            line.trim(),
+            options.isProtein,
+            inclusive1BasedStart,
+            inclusive1BasedEnd
+          )
+        );
         lastLineWasLocation = true;
       } else {
         if (currentFeatureNote) {
@@ -20129,7 +20161,14 @@ function genbankToJson(string, options = {}) {
         const feat = getCurrentFeature();
         feat.type = key;
         feat.strand = strand;
-        parseFeatureLocation(val2, options);
+        feat.locations = feat.locations.concat(
+          parseFeatureLocation(
+            val2,
+            options.isProtein,
+            inclusive1BasedStart,
+            inclusive1BasedEnd
+          )
+        );
         lastLineWasLocation = true;
       }
     }
@@ -20152,29 +20191,6 @@ function genbankToJson(string, options = {}) {
     return qual;
   }
   __name(isNote, "isNote");
-  function parseFeatureLocation(locStr, options2) {
-    locStr = locStr.trim();
-    const locArr = [];
-    locStr.replace(/(\d+)/g, function(string2, match) {
-      locArr.push(match);
-    });
-    for (let i = 0; i < locArr.length; i += 2) {
-      const start = parseInt(locArr[i], 10) - (inclusive1BasedStart ? 0 : 1);
-      let end = parseInt(locArr[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
-      if (isNaN(end)) {
-        end = start;
-      }
-      const location = {
-        start,
-        end
-      };
-      const feat = getCurrentFeature();
-      feat.locations.push(
-        options2.isProtein ? convertAACaretPositionOrRangeToDna(location) : location
-      );
-    }
-  }
-  __name(parseFeatureLocation, "parseFeatureLocation");
   function parseFeatureNote(line) {
     let newLine;
     newLine = line.trimLeft();
@@ -32765,6 +32781,7 @@ exports.jsonToBed = jsonToBed;
 exports.jsonToFasta = jsonToFasta;
 exports.jsonToGenbank = jsonToGenbank;
 exports.jsonToJsonString = jsonToJsonString;
+exports.parseFeatureLocation = parseFeatureLocation;
 exports.parseUracilFeatures = parseUracilFeatures;
 exports.sbolXmlToJson = sbolXmlToJson;
 exports.searchWholeObjByName = searchWholeObjByName;

package/index.mjs

@@ -19777,6 +19777,30 @@ function flattenSequenceArray(parsingResultArray, opts) {
   return parsingResultArray;
 }
 __name(flattenSequenceArray, "flattenSequenceArray");
+function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd) {
+  locStr = locStr.trim();
+  const locArr = [];
+  locStr.replace(/(\d+)/g, function(string, match) {
+    locArr.push(match);
+  });
+  const locArray = [];
+  for (let i = 0; i < locArr.length; i += 2) {
+    const start = parseInt(locArr[i], 10) - (inclusive1BasedStart ? 0 : 1);
+    let end = parseInt(locArr[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
+    if (isNaN(end)) {
+      end = start;
+    }
+    const location = {
+      start,
+      end
+    };
+    locArray.push(
+      isProtein ? convertAACaretPositionOrRangeToDna(location) : location
+    );
+  }
+  return locArray;
+}
+__name(parseFeatureLocation, "parseFeatureLocation");
 function genbankToJson(string, options = {}) {
   const {
     inclusive1BasedStart,
@@ -20101,7 +20125,15 @@ function genbankToJson(string, options = {}) {
     }
     if (isFeatureLineRunon(line, featureLocationIndentation)) {
       if (lastLineWasLocation) {
-        parseFeatureLocation(line.trim(), options);
+        const feat = getCurrentFeature();
+        feat.locations = feat.locations.concat(
+          parseFeatureLocation(
+            line.trim(),
+            options.isProtein,
+            inclusive1BasedStart,
+            inclusive1BasedEnd
+          )
+        );
         lastLineWasLocation = true;
       } else {
         if (currentFeatureNote) {
@@ -20127,7 +20159,14 @@ function genbankToJson(string, options = {}) {
         const feat = getCurrentFeature();
         feat.type = key;
         feat.strand = strand;
-        parseFeatureLocation(val2, options);
+        feat.locations = feat.locations.concat(
+          parseFeatureLocation(
+            val2,
+            options.isProtein,
+            inclusive1BasedStart,
+            inclusive1BasedEnd
+          )
+        );
         lastLineWasLocation = true;
       }
     }
@@ -20150,29 +20189,6 @@ function genbankToJson(string, options = {}) {
     return qual;
   }
   __name(isNote, "isNote");
-  function parseFeatureLocation(locStr, options2) {
-    locStr = locStr.trim();
-    const locArr = [];
-    locStr.replace(/(\d+)/g, function(string2, match) {
-      locArr.push(match);
-    });
-    for (let i = 0; i < locArr.length; i += 2) {
-      const start = parseInt(locArr[i], 10) - (inclusive1BasedStart ? 0 : 1);
-      let end = parseInt(locArr[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
-      if (isNaN(end)) {
-        end = start;
-      }
-      const location = {
-        start,
-        end
-      };
-      const feat = getCurrentFeature();
-      feat.locations.push(
-        options2.isProtein ? convertAACaretPositionOrRangeToDna(location) : location
-      );
-    }
-  }
-  __name(parseFeatureLocation, "parseFeatureLocation");
   function parseFeatureNote(line) {
     let newLine;
     newLine = line.trimLeft();
@@ -32764,6 +32780,7 @@ export {
   jsonToFasta,
   jsonToGenbank,
   jsonToJsonString,
+  parseFeatureLocation,
   parseUracilFeatures,
   sbolXmlToJson,
   searchWholeObjByName,

package/index.umd.js

@@ -19781,6 +19781,30 @@ var __async = (__this, __arguments, generator) => {
     return parsingResultArray;
   }
   __name(flattenSequenceArray, "flattenSequenceArray");
+  function parseFeatureLocation(locStr, isProtein, inclusive1BasedStart, inclusive1BasedEnd) {
+    locStr = locStr.trim();
+    const locArr = [];
+    locStr.replace(/(\d+)/g, function(string, match) {
+      locArr.push(match);
+    });
+    const locArray = [];
+    for (let i2 = 0; i2 < locArr.length; i2 += 2) {
+      const start = parseInt(locArr[i2], 10) - (inclusive1BasedStart ? 0 : 1);
+      let end = parseInt(locArr[i2 + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
+      if (isNaN(end)) {
+        end = start;
+      }
+      const location = {
+        start,
+        end
+      };
+      locArray.push(
+        isProtein ? convertAACaretPositionOrRangeToDna(location) : location
+      );
+    }
+    return locArray;
+  }
+  __name(parseFeatureLocation, "parseFeatureLocation");
   function genbankToJson(string, options = {}) {
     const {
       inclusive1BasedStart,
@@ -20105,7 +20129,15 @@ var __async = (__this, __arguments, generator) => {
       }
       if (isFeatureLineRunon(line, featureLocationIndentation)) {
         if (lastLineWasLocation) {
-          parseFeatureLocation(line.trim(), options);
+          const feat = getCurrentFeature();
+          feat.locations = feat.locations.concat(
+            parseFeatureLocation(
+              line.trim(),
+              options.isProtein,
+              inclusive1BasedStart,
+              inclusive1BasedEnd
+            )
+          );
           lastLineWasLocation = true;
         } else {
           if (currentFeatureNote) {
@@ -20131,7 +20163,14 @@ var __async = (__this, __arguments, generator) => {
           const feat = getCurrentFeature();
           feat.type = key;
           feat.strand = strand;
-          parseFeatureLocation(val2, options);
+          feat.locations = feat.locations.concat(
+            parseFeatureLocation(
+              val2,
+              options.isProtein,
+              inclusive1BasedStart,
+              inclusive1BasedEnd
+            )
+          );
           lastLineWasLocation = true;
         }
       }
@@ -20154,29 +20193,6 @@ var __async = (__this, __arguments, generator) => {
       return qual;
     }
     __name(isNote, "isNote");
-    function parseFeatureLocation(locStr, options2) {
-      locStr = locStr.trim();
-      const locArr = [];
-      locStr.replace(/(\d+)/g, function(string2, match) {
-        locArr.push(match);
-      });
-      for (let i2 = 0; i2 < locArr.length; i2 += 2) {
-        const start = parseInt(locArr[i2], 10) - (inclusive1BasedStart ? 0 : 1);
-        let end = parseInt(locArr[i2 + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
-        if (isNaN(end)) {
-          end = start;
-        }
-        const location = {
-          start,
-          end
-        };
-        const feat = getCurrentFeature();
-        feat.locations.push(
-          options2.isProtein ? convertAACaretPositionOrRangeToDna(location) : location
-        );
-      }
-    }
-    __name(parseFeatureLocation, "parseFeatureLocation");
     function parseFeatureNote(line) {
       let newLine;
       newLine = line.trimLeft();
@@ -32767,6 +32783,7 @@ ${seq.sequence}
   exports2.jsonToFasta = jsonToFasta;
   exports2.jsonToGenbank = jsonToGenbank;
   exports2.jsonToJsonString = jsonToJsonString;
+  exports2.parseFeatureLocation = parseFeatureLocation;
   exports2.parseUracilFeatures = parseUracilFeatures;
   exports2.sbolXmlToJson = sbolXmlToJson;
   exports2.searchWholeObjByName = searchWholeObjByName;

package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.3",
+  "version": "0.4.5",
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.11",
+    "@teselagen/sequence-utils": "0.3.12",
     "@teselagen/range-utils": "0.3.7",
     "@gmod/gff": "^1.2.1",
     "buffer": "^6.0.3",

package/src/genbankToJson.js

@@ -8,6 +8,40 @@ import splitStringIntoLines from "./utils/splitStringIntoLines.js";
 
 import createInitialSequence from "./utils/createInitialSequence";
 
+export function parseFeatureLocation(
+  locStr,
+  isProtein,
+  inclusive1BasedStart,
+  inclusive1BasedEnd
+) {
+  locStr = locStr.trim();
+  const locArr = [];
+  locStr.replace(/(\d+)/g, function (string, match) {
+    locArr.push(match);
+  });
+  const locArray = [];
+  for (let i = 0; i < locArr.length; i += 2) {
+    const start = parseInt(locArr[i], 10) - (inclusive1BasedStart ? 0 : 1);
+    let end = parseInt(locArr[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
+    if (isNaN(end)) {
+      //if no end is supplied, assume that the end should be set to whatever the start is
+      //this makes a feature location passed as:
+      //147
+      //function like:
+      //147..147
+      end = start;
+    }
+    const location = {
+      start: start,
+      end: end
+    };
+    locArray.push(
+      isProtein ? convertAACaretPositionOrRangeToDna(location) : location
+    );
+  }
+  return locArray;
+}
+
 function genbankToJson(string, options = {}) {
   const {
     inclusive1BasedStart,
@@ -428,7 +462,15 @@ function genbankToJson(string, options = {}) {
       //the line is a continuation of the above line
       if (lastLineWasLocation) {
         //the last line was a location, so the run-on line is expected to be a feature location as well
-        parseFeatureLocation(line.trim(), options);
+        const feat = getCurrentFeature();
+        feat.locations = feat.locations.concat(
+          parseFeatureLocation(
+            line.trim(),
+            options.isProtein,
+            inclusive1BasedStart,
+            inclusive1BasedEnd
+          )
+        );
         lastLineWasLocation = true;
       } else {
         //the last line was a note
@@ -466,8 +508,14 @@ function genbankToJson(string, options = {}) {
         const feat = getCurrentFeature();
         feat.type = key;
         feat.strand = strand;
-
-        parseFeatureLocation(val, options);
+        feat.locations = feat.locations.concat(
+          parseFeatureLocation(
+            val,
+            options.isProtein,
+            inclusive1BasedStart,
+            inclusive1BasedEnd
+          )
+        );
         lastLineWasLocation = true;
       }
     }
@@ -495,36 +543,6 @@ function genbankToJson(string, options = {}) {
     return qual;
   }
 
-  function parseFeatureLocation(locStr, options) {
-    locStr = locStr.trim();
-    const locArr = [];
-    locStr.replace(/(\d+)/g, function (string, match) {
-      locArr.push(match);
-    });
-    for (let i = 0; i < locArr.length; i += 2) {
-      const start = parseInt(locArr[i], 10) - (inclusive1BasedStart ? 0 : 1);
-      let end = parseInt(locArr[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
-      if (isNaN(end)) {
-        //if no end is supplied, assume that the end should be set to whatever the start is
-        //this makes a feature location passed as:
-        //147
-        //function like:
-        //147..147
-        end = start;
-      }
-      const location = {
-        start: start,
-        end: end
-      };
-      const feat = getCurrentFeature();
-      feat.locations.push(
-        options.isProtein
-          ? convertAACaretPositionOrRangeToDna(location)
-          : location
-      );
-    }
-  }
-
   function parseFeatureNote(line) {
     let newLine;
 

package/src/index.js

@@ -1,6 +1,6 @@
 export { default as anyToJson } from "./anyToJson";
 export { default as fastaToJson } from "./fastaToJson";
-export { default as genbankToJson } from "./genbankToJson";
+export { default as genbankToJson, parseFeatureLocation } from "./genbankToJson";
 export { default as sbolXmlToJson } from "./sbolXmlToJson";
 export { default as geneiousXmlToJson } from "./geneiousXmlToJson";
 export { default as jbeiXmlToJson } from "./jbeiXmlToJson";