@teselagen/bio-parsers 0.4.5 → 0.4.7

package/index.js

@@ -948,7 +948,7 @@ lodash.exports;
     }
     __name(unicodeWords, "unicodeWords");
     var runInContext = /* @__PURE__ */ __name(function runInContext2(context) {
-      context = context == null ? root : _2.defaults(root.Object(), context, _2.pick(root, contextProps));
+      context = context == null ? root : _.defaults(root.Object(), context, _.pick(root, contextProps));
       var Array2 = context.Array, Date2 = context.Date, Error2 = context.Error, Function2 = context.Function, Math2 = context.Math, Object2 = context.Object, RegExp2 = context.RegExp, String2 = context.String, TypeError2 = context.TypeError;
       var arrayProto = Array2.prototype, funcProto = Function2.prototype, objectProto = Object2.prototype;
       var coreJsData = context["__core-js_shared__"];
@@ -6159,17 +6159,16 @@ lodash.exports;
       }
       return lodash2;
     }, "runInContext");
-    var _2 = runInContext();
+    var _ = runInContext();
     if (freeModule) {
-      (freeModule.exports = _2)._ = _2;
-      freeExports._ = _2;
+      (freeModule.exports = _)._ = _;
+      freeExports._ = _;
     } else {
-      root._ = _2;
+      root._ = _;
     }
   }).call(commonjsGlobal);
 })(lodash, lodash.exports);
 var lodashExports = lodash.exports;
-const _ = /* @__PURE__ */ getDefaultExportFromCjs(lodashExports);
 const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
 const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
 const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
@@ -11275,7 +11274,7 @@ const annotationTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, {
+function filterSequenceString(sequenceString = "", {
   additionalValidChars = "",
   isOligo,
   name,
@@ -19447,12 +19446,6 @@ function validateSequence(sequence, options = {}) {
     sequence.proteinSize = sequence.proteinSequence.length;
   } else {
     const temp = sequence.sequence;
-    if (!sequence.isOligo) {
-      sequence.sequence = sequence.sequence.replace(
-        /u/gi,
-        (u) => u === "U" ? "T" : "t"
-      );
-    }
     if (temp !== sequence.sequence && !sequence.isDNA && !sequence.isProtein && sequence.isRNA !== false) {
       sequence.type = "RNA";
       sequence.sequence = temp;
@@ -26909,7 +26902,7 @@ function requireBuffer_list() {
       // Make sure the linked list only shows the minimal necessary information.
     }, {
       key: custom,
-      value: /* @__PURE__ */ __name(function value(_2, options) {
+      value: /* @__PURE__ */ __name(function value(_, options) {
         return inspect(this, _objectSpread(_objectSpread({}, options), {}, {
           // Only inspect one level.
           depth: 0,
@@ -27205,7 +27198,7 @@ function requireBrowser() {
     try {
       if (!commonjsGlobal.localStorage)
         return false;
-    } catch (_2) {
+    } catch (_) {
       return false;
     }
     var val2 = commonjsGlobal.localStorage[name];
@@ -27313,7 +27306,7 @@ function require_stream_writable() {
           return this.getBuffer();
         }, "writableStateBufferGetter"), "_writableState.buffer is deprecated. Use _writableState.getBuffer instead.", "DEP0003")
       });
-    } catch (_2) {
+    } catch (_) {
     }
   })();
   var realHasInstance;
@@ -29935,7 +29928,7 @@ function gffToJson(string) {
       if (!features[feature.seq_id])
         features[feature.seq_id] = [];
       const attributes = feature.attributes || {};
-      const name = _.get(attributes, "ID[0]");
+      const name = lodashExports.get(attributes, "ID[0]");
       features[feature.seq_id].push({
         name,
         start: feature.start,

package/index.mjs

@@ -946,7 +946,7 @@ lodash.exports;
     }
     __name(unicodeWords, "unicodeWords");
     var runInContext = /* @__PURE__ */ __name(function runInContext2(context) {
-      context = context == null ? root : _2.defaults(root.Object(), context, _2.pick(root, contextProps));
+      context = context == null ? root : _.defaults(root.Object(), context, _.pick(root, contextProps));
       var Array2 = context.Array, Date2 = context.Date, Error2 = context.Error, Function2 = context.Function, Math2 = context.Math, Object2 = context.Object, RegExp2 = context.RegExp, String2 = context.String, TypeError2 = context.TypeError;
       var arrayProto = Array2.prototype, funcProto = Function2.prototype, objectProto = Object2.prototype;
       var coreJsData = context["__core-js_shared__"];
@@ -6157,17 +6157,16 @@ lodash.exports;
       }
       return lodash2;
     }, "runInContext");
-    var _2 = runInContext();
+    var _ = runInContext();
     if (freeModule) {
-      (freeModule.exports = _2)._ = _2;
-      freeExports._ = _2;
+      (freeModule.exports = _)._ = _;
+      freeExports._ = _;
     } else {
-      root._ = _2;
+      root._ = _;
     }
   }).call(commonjsGlobal);
 })(lodash, lodash.exports);
 var lodashExports = lodash.exports;
-const _ = /* @__PURE__ */ getDefaultExportFromCjs(lodashExports);
 const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
 const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
 const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
@@ -11273,7 +11272,7 @@ const annotationTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, {
+function filterSequenceString(sequenceString = "", {
   additionalValidChars = "",
   isOligo,
   name,
@@ -19445,12 +19444,6 @@ function validateSequence(sequence, options = {}) {
     sequence.proteinSize = sequence.proteinSequence.length;
   } else {
     const temp = sequence.sequence;
-    if (!sequence.isOligo) {
-      sequence.sequence = sequence.sequence.replace(
-        /u/gi,
-        (u) => u === "U" ? "T" : "t"
-      );
-    }
     if (temp !== sequence.sequence && !sequence.isDNA && !sequence.isProtein && sequence.isRNA !== false) {
       sequence.type = "RNA";
       sequence.sequence = temp;
@@ -26907,7 +26900,7 @@ function requireBuffer_list() {
       // Make sure the linked list only shows the minimal necessary information.
     }, {
       key: custom,
-      value: /* @__PURE__ */ __name(function value(_2, options) {
+      value: /* @__PURE__ */ __name(function value(_, options) {
         return inspect(this, _objectSpread(_objectSpread({}, options), {}, {
           // Only inspect one level.
           depth: 0,
@@ -27203,7 +27196,7 @@ function requireBrowser() {
     try {
       if (!commonjsGlobal.localStorage)
         return false;
-    } catch (_2) {
+    } catch (_) {
       return false;
     }
     var val2 = commonjsGlobal.localStorage[name];
@@ -27311,7 +27304,7 @@ function require_stream_writable() {
           return this.getBuffer();
         }, "writableStateBufferGetter"), "_writableState.buffer is deprecated. Use _writableState.getBuffer instead.", "DEP0003")
       });
-    } catch (_2) {
+    } catch (_) {
     }
   })();
   var realHasInstance;
@@ -29933,7 +29926,7 @@ function gffToJson(string) {
       if (!features[feature.seq_id])
         features[feature.seq_id] = [];
       const attributes = feature.attributes || {};
-      const name = _.get(attributes, "ID[0]");
+      const name = lodashExports.get(attributes, "ID[0]");
       features[feature.seq_id].push({
         name,
         start: feature.start,

package/index.umd.js

@@ -950,7 +950,7 @@ var __async = (__this, __arguments, generator) => {
       }
       __name(unicodeWords, "unicodeWords");
       var runInContext = /* @__PURE__ */ __name(function runInContext2(context) {
-        context = context == null ? root : _2.defaults(root.Object(), context, _2.pick(root, contextProps));
+        context = context == null ? root : _.defaults(root.Object(), context, _.pick(root, contextProps));
         var Array2 = context.Array, Date2 = context.Date, Error2 = context.Error, Function2 = context.Function, Math2 = context.Math, Object2 = context.Object, RegExp2 = context.RegExp, String2 = context.String, TypeError2 = context.TypeError;
         var arrayProto = Array2.prototype, funcProto = Function2.prototype, objectProto = Object2.prototype;
         var coreJsData = context["__core-js_shared__"];
@@ -6161,17 +6161,16 @@ var __async = (__this, __arguments, generator) => {
         }
         return lodash2;
       }, "runInContext");
-      var _2 = runInContext();
+      var _ = runInContext();
       if (freeModule) {
-        (freeModule.exports = _2)._ = _2;
-        freeExports._ = _2;
+        (freeModule.exports = _)._ = _;
+        freeExports._ = _;
       } else {
-        root._ = _2;
+        root._ = _;
       }
     }).call(commonjsGlobal);
   })(lodash, lodash.exports);
   var lodashExports = lodash.exports;
-  const _ = /* @__PURE__ */ getDefaultExportFromCjs(lodashExports);
   const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
   const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
   const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
@@ -11277,7 +11276,7 @@ var __async = (__this, __arguments, generator) => {
     "primers",
     "guides"
   ];
-  function filterSequenceString(sequenceString, {
+  function filterSequenceString(sequenceString = "", {
     additionalValidChars = "",
     isOligo,
     name: name2,
@@ -19449,12 +19448,6 @@ var __async = (__this, __arguments, generator) => {
       sequence.proteinSize = sequence.proteinSequence.length;
     } else {
       const temp = sequence.sequence;
-      if (!sequence.isOligo) {
-        sequence.sequence = sequence.sequence.replace(
-          /u/gi,
-          (u) => u === "U" ? "T" : "t"
-        );
-      }
       if (temp !== sequence.sequence && !sequence.isDNA && !sequence.isProtein && sequence.isRNA !== false) {
         sequence.type = "RNA";
         sequence.sequence = temp;
@@ -26911,7 +26904,7 @@ var __async = (__this, __arguments, generator) => {
         // Make sure the linked list only shows the minimal necessary information.
       }, {
         key: custom,
-        value: /* @__PURE__ */ __name(function value(_2, options) {
+        value: /* @__PURE__ */ __name(function value(_, options) {
           return inspect(this, _objectSpread(_objectSpread({}, options), {}, {
             // Only inspect one level.
             depth: 0,
@@ -27207,7 +27200,7 @@ var __async = (__this, __arguments, generator) => {
       try {
         if (!commonjsGlobal.localStorage)
           return false;
-      } catch (_2) {
+      } catch (_) {
         return false;
       }
       var val2 = commonjsGlobal.localStorage[name2];
@@ -27315,7 +27308,7 @@ var __async = (__this, __arguments, generator) => {
             return this.getBuffer();
           }, "writableStateBufferGetter"), "_writableState.buffer is deprecated. Use _writableState.getBuffer instead.", "DEP0003")
         });
-      } catch (_2) {
+      } catch (_) {
       }
     })();
     var realHasInstance;
@@ -29937,7 +29930,7 @@ ${seq.sequence}
         if (!features[feature.seq_id])
           features[feature.seq_id] = [];
         const attributes = feature.attributes || {};
-        const name2 = _.get(attributes, "ID[0]");
+        const name2 = lodashExports.get(attributes, "ID[0]");
         features[feature.seq_id].push({
           name: name2,
           start: feature.start,

package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.5",
+  "version": "0.4.7",
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.12",
+    "@teselagen/sequence-utils": "0.3.13",
     "@teselagen/range-utils": "0.3.7",
     "@gmod/gff": "^1.2.1",
     "buffer": "^6.0.3",

package/src/gffToJson.js

@@ -1,5 +1,5 @@
 import gff from "@gmod/gff";
-import _ from "lodash";
+import { get } from "lodash";
 
 function gffToJson(string) {
   const arrayOfThings = gff.parseStringSync(string);
@@ -13,7 +13,7 @@ function gffToJson(string) {
       const feature = featureOrSeq[0];
       if (!features[feature.seq_id]) features[feature.seq_id] = [];
       const attributes = feature.attributes || {};
-      const name = _.get(attributes, "ID[0]");
+      const name = get(attributes, "ID[0]");
       features[feature.seq_id].push({
         name,
         start: feature.start,

package/src/utils/validateSequence.js

@@ -110,11 +110,6 @@ export default function validateSequence(sequence, options = {}) {
   } else {
     //todo: this logic won't catch every case of RNA, so we should probably handle RNA conversion at another level..
     const temp = sequence.sequence;
-    if (!sequence.isOligo) {
-      sequence.sequence = sequence.sequence.replace(/u/gi, u =>
-        u === "U" ? "T" : "t"
-      );
-    }
     if (
       temp !== sequence.sequence &&
       !sequence.isDNA &&