@teselagen/bio-parsers 0.4.6 → 0.4.7

package/index.js

@@ -11274,7 +11274,7 @@ const annotationTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, {
+function filterSequenceString(sequenceString = "", {
   additionalValidChars = "",
   isOligo,
   name,
@@ -19446,12 +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;

package/index.mjs

@@ -11272,7 +11272,7 @@ const annotationTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, {
+function filterSequenceString(sequenceString = "", {
   additionalValidChars = "",
   isOligo,
   name,
@@ -19444,12 +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;

package/index.umd.js

@@ -11276,7 +11276,7 @@ var __async = (__this, __arguments, generator) => {
     "primers",
     "guides"
   ];
-  function filterSequenceString(sequenceString, {
+  function filterSequenceString(sequenceString = "", {
     additionalValidChars = "",
     isOligo,
     name: name2,
@@ -19448,12 +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;

package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.6",
+  "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 {get} from "lodash";
+import { get } from "lodash";
 
 function gffToJson(string) {
   const arrayOfThings = gff.parseStringSync(string);

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 &&