@teselagen/sequence-utils 0.3.41 → 0.3.42

package/README.md

@@ -64,15 +64,9 @@ Make sure they pass by running `npm test`
 
 Commit and push all changes first (make sure tests are passing!)
 
-### Teselagen collaborators:
+# Publishing
 
-Commit and push all changes
-Sign into npm using the teselagen npm account (npm whoami)
-
-```
-npm version patch|minor|major
-npm publish
-```
+See the [README](../README.md)
 
 ### Outside collaborators:
 

package/filterSequenceString.d.ts

@@ -1,4 +1,4 @@
-export default function filterSequenceString(sequenceString?: string, { additionalValidChars, isOligo, name, isProtein, isRna, isMixedRnaAndDna }?: {
+export default function filterSequenceString(sequenceString?: string, { additionalValidChars, isOligo, name, isProtein, isRna, isMixedRnaAndDna, getAcceptedInsertChars }?: {
     additionalValidChars?: string | undefined;
 }): (string | string[])[];
 export function getAcceptedChars({ isOligo, isProtein, isRna, isMixedRnaAndDna }?: {}): string;

package/index.cjs

@@ -6196,14 +6196,16 @@ function filterSequenceString(sequenceString = "", {
   name,
   isProtein,
   isRna,
-  isMixedRnaAndDna
+  isMixedRnaAndDna,
+  getAcceptedInsertChars
 } = {}) {
-  const acceptedChars = getAcceptedChars({
+  const sequenceTypeInfo = {
     isOligo,
     isProtein,
     isRna,
     isMixedRnaAndDna
-  });
+  };
+  const acceptedChars = isFunction(getAcceptedInsertChars) ? getAcceptedInsertChars(sequenceTypeInfo) : getAcceptedChars(sequenceTypeInfo);
   const replaceChars = getReplaceChars({
     isOligo,
     isProtein,
@@ -6440,6 +6442,7 @@ function tidyUpSequenceData(pSeqData, options = {}) {
     doNotProvideIdsForAnnotations,
     noCdsTranslations,
     convertAnnotationsFromAAIndices,
+    getAcceptedInsertChars,
     topLevelSeqData
   } = options;
   let seqData = cloneDeep(pSeqData);
@@ -6471,13 +6474,16 @@ function tidyUpSequenceData(pSeqData, options = {}) {
   if (!doNotRemoveInvalidChars) {
     if (seqData.isProtein) {
       const [newSeq] = filterSequenceString(seqData.proteinSequence, __spreadProps(__spreadValues({}, topLevelSeqData || seqData), {
-        isProtein: true
+        isProtein: true,
+        getAcceptedInsertChars
       }));
       seqData.proteinSequence = newSeq;
     } else {
-      const [newSeq] = filterSequenceString(seqData.sequence, __spreadValues({
+      const [newSeq] = filterSequenceString(seqData.sequence, __spreadProps(__spreadValues({
         additionalValidChars
-      }, topLevelSeqData || seqData));
+      }, topLevelSeqData || seqData), {
+        getAcceptedInsertChars
+      }));
       seqData.sequence = newSeq;
     }
   }

package/index.js

@@ -6194,14 +6194,16 @@ function filterSequenceString(sequenceString = "", {
   name,
   isProtein,
   isRna,
-  isMixedRnaAndDna
+  isMixedRnaAndDna,
+  getAcceptedInsertChars
 } = {}) {
-  const acceptedChars = getAcceptedChars({
+  const sequenceTypeInfo = {
     isOligo,
     isProtein,
     isRna,
     isMixedRnaAndDna
-  });
+  };
+  const acceptedChars = isFunction(getAcceptedInsertChars) ? getAcceptedInsertChars(sequenceTypeInfo) : getAcceptedChars(sequenceTypeInfo);
   const replaceChars = getReplaceChars({
     isOligo,
     isProtein,
@@ -6438,6 +6440,7 @@ function tidyUpSequenceData(pSeqData, options = {}) {
     doNotProvideIdsForAnnotations,
     noCdsTranslations,
     convertAnnotationsFromAAIndices,
+    getAcceptedInsertChars,
     topLevelSeqData
   } = options;
   let seqData = cloneDeep(pSeqData);
@@ -6469,13 +6472,16 @@ function tidyUpSequenceData(pSeqData, options = {}) {
   if (!doNotRemoveInvalidChars) {
     if (seqData.isProtein) {
       const [newSeq] = filterSequenceString(seqData.proteinSequence, __spreadProps(__spreadValues({}, topLevelSeqData || seqData), {
-        isProtein: true
+        isProtein: true,
+        getAcceptedInsertChars
       }));
       seqData.proteinSequence = newSeq;
     } else {
-      const [newSeq] = filterSequenceString(seqData.sequence, __spreadValues({
+      const [newSeq] = filterSequenceString(seqData.sequence, __spreadProps(__spreadValues({
         additionalValidChars
-      }, topLevelSeqData || seqData));
+      }, topLevelSeqData || seqData), {
+        getAcceptedInsertChars
+      }));
       seqData.sequence = newSeq;
     }
   }

package/index.umd.cjs

@@ -6198,14 +6198,16 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     name,
     isProtein,
     isRna,
-    isMixedRnaAndDna
+    isMixedRnaAndDna,
+    getAcceptedInsertChars
   } = {}) {
-    const acceptedChars = getAcceptedChars({
+    const sequenceTypeInfo = {
       isOligo,
       isProtein,
       isRna,
       isMixedRnaAndDna
-    });
+    };
+    const acceptedChars = isFunction(getAcceptedInsertChars) ? getAcceptedInsertChars(sequenceTypeInfo) : getAcceptedChars(sequenceTypeInfo);
     const replaceChars = getReplaceChars({
       isOligo,
       isProtein,
@@ -6442,6 +6444,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       doNotProvideIdsForAnnotations,
       noCdsTranslations,
       convertAnnotationsFromAAIndices,
+      getAcceptedInsertChars,
       topLevelSeqData
     } = options;
     let seqData = cloneDeep(pSeqData);
@@ -6473,13 +6476,16 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     if (!doNotRemoveInvalidChars) {
       if (seqData.isProtein) {
         const [newSeq] = filterSequenceString(seqData.proteinSequence, __spreadProps(__spreadValues({}, topLevelSeqData || seqData), {
-          isProtein: true
+          isProtein: true,
+          getAcceptedInsertChars
         }));
         seqData.proteinSequence = newSeq;
       } else {
-        const [newSeq] = filterSequenceString(seqData.sequence, __spreadValues({
+        const [newSeq] = filterSequenceString(seqData.sequence, __spreadProps(__spreadValues({
           additionalValidChars
-        }, topLevelSeqData || seqData));
+        }, topLevelSeqData || seqData), {
+          getAcceptedInsertChars
+        }));
         seqData.sequence = newSeq;
       }
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.41",
+  "version": "0.3.42",
   "repository": "https://github.com/TeselaGen/tg-oss",
   "type": "module",
   "dependencies": {
@@ -9,7 +9,7 @@
     "string-splice": "^1.3.0",
     "lodash-es": "^4.17.21",
     "shortid": "2.2.16",
-    "@teselagen/range-utils": "0.3.18"
+    "@teselagen/range-utils": "0.3.20"
   },
   "exports": {
     ".": {

package/src/filterSequenceString.js

@@ -4,6 +4,7 @@ import {
   ambiguous_rna_letters,
   extended_protein_letters
 } from "./bioData";
+import {isFunction} from "lodash-es";
 
 let allWarnings = [];
 
@@ -30,15 +31,17 @@ export default function filterSequenceString(
     name,
     isProtein,
     isRna,
-    isMixedRnaAndDna
-  } = {}
+    isMixedRnaAndDna,
+    getAcceptedInsertChars
+  } = {},
 ) {
-  const acceptedChars = getAcceptedChars({
+  const sequenceTypeInfo = {
     isOligo,
     isProtein,
     isRna,
     isMixedRnaAndDna
-  });
+  };
+  const acceptedChars = isFunction(getAcceptedInsertChars) ? getAcceptedInsertChars(sequenceTypeInfo) : getAcceptedChars(sequenceTypeInfo);
   const replaceChars = getReplaceChars({
     isOligo,
     isProtein,

package/src/tidyUpSequenceData.js

@@ -22,6 +22,7 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
     doNotProvideIdsForAnnotations,
     noCdsTranslations,
     convertAnnotationsFromAAIndices,
+    getAcceptedInsertChars,
     topLevelSeqData
   } = options;
   let seqData = cloneDeep(pSeqData); //sequence is usually immutable, so we clone it and return it
@@ -59,13 +60,15 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
     if (seqData.isProtein) {
       const [newSeq] = filterSequenceString(seqData.proteinSequence, {
         ...(topLevelSeqData || seqData),
-        isProtein: true
+        isProtein: true,
+        getAcceptedInsertChars
       });
       seqData.proteinSequence = newSeq;
     } else {
       const [newSeq] = filterSequenceString(seqData.sequence, {
         additionalValidChars,
-        ...(topLevelSeqData || seqData)
+        ...(topLevelSeqData || seqData),
+        getAcceptedInsertChars
       });
       seqData.sequence = newSeq;
     }