Merge pull request #1 from PerkinElmer/CLN-54033

CLN-54033: support RNA sequence
Revvity · Jul 24, 2023 · 42aaa83 · 42aaa83
2 parents 9078f64 + 62dd54e
commit 42aaa83
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/packages/bio-parsers/src/genbankToJson.js b/packages/bio-parsers/src/genbankToJson.js
@@ -338,7 +338,7 @@ function genbankToJson(string, options = {}) {
 
       if (
         j === 4 &&
-        (item.match(/ds-dna/i) || item.match(/ss-dna/i) || item.match(/dna/i))
+        (item.match(/ds-dna/i) || item.match(/ss-dna/i) || item.match(/dna/i) || item.match(/rna/i))
       ) {
         if (options.isProtein === undefined) {
           options.isProtein = false;
@@ -347,6 +347,9 @@ function genbankToJson(string, options = {}) {
         if (item.match(/ss-dna/i)) {
           options.isSingleStrandedDNA = true;
         }
+        if (item.match(/rna/i) && !item.match(/ss-rna/i)) {
+          options.isDoubleStrandedRNA = true;
+        }
       }
 
       // Division
@@ -368,6 +371,7 @@ function genbankToJson(string, options = {}) {
     result.parsedSequence.gbDivision = gbDivision;
     result.parsedSequence.sequenceTypeFromLocus = options.sequenceTypeFromLocus;
     result.parsedSequence.isSingleStrandedDNA = options.isSingleStrandedDNA;
+    result.parsedSequence.isDoubleStrandedRNA = options.isDoubleStrandedRNA;
     result.parsedSequence.date = date;
     result.parsedSequence.circular = circular;
   }

diff --git a/packages/sequence-utils/src/getComplementSequenceString.js b/packages/sequence-utils/src/getComplementSequenceString.js
@@ -1,12 +1,14 @@
 import DNAComplementMap from "./DNAComplementMap";
+import { merge } from "lodash";
 
 
 // ac.throw([ac.string,ac.bool],arguments);
-export default function getComplementSequenceString(sequence) {
+export default function getComplementSequenceString(sequence, isRna) {
   // ac.throw([ac.string],arguments);
   let complementSeqString = "";
+  const complementMap = isRna ? merge(DNAComplementMap, { a: 'u', A: 'U'}) : DNAComplementMap;
   for (let i = 0; i < sequence.length; i++) {
-    let complementChar = DNAComplementMap[sequence[i]];
+    let complementChar = complementMap[sequence[i]];
     if (!complementChar) {
       complementChar = sequence[i];
       // throw new Error('trying to get the reverse compelement of an invalid base');