Added menu item to allow user to export DNA as FASTA when looking at …

…a protein sequence to resolve TeselaGen#61
ryan-stackwave · Feb 27, 2024 · 8f1b721 · 8f1b721
1 parent bd91195
commit 8f1b721
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Showing 6 changed files with 27 additions and 17 deletions.
diff --git a/packages/bio-parsers/src/jsonToFasta.js b/packages/bio-parsers/src/jsonToFasta.js
@@ -17,7 +17,7 @@ export default function jsonToFasta(jsonSequence, options) {
   options = options || {};
   let seqToUse = sequence;
   let sizeToUse = size;
-  if (isProtein && proteinSequence) {
+  if (isProtein && proteinSequence && !options?.useDNA) {
     seqToUse = proteinSequence;
     sizeToUse = proteinSize;
   }

diff --git a/packages/ove/src/MenuBar/defaultConfig.js b/packages/ove/src/MenuBar/defaultConfig.js
@@ -42,6 +42,7 @@ export default [
         submenu: [
           { cmd: "exportSequenceAsGenbank" },
           { cmd: "exportSequenceAsFasta" },
+          { cmd: "exportDNASequenceAsFasta" },
           { cmd: "exportSequenceAsTeselagenJson" }
         ]
       },

diff --git a/packages/ove/src/SimpleCircularOrLinearView.js b/packages/ove/src/SimpleCircularOrLinearView.js
@@ -102,8 +102,8 @@ export default props => {
   )
     ? CircularView
     : _sequenceData.isOligo && _sequenceData.sequence
-    ? SimpleOligoPreview
-    : LinearView;
+      ? SimpleOligoPreview
+      : LinearView;
   if (withChoosePreviewType && previewType === "row") {
     Component = RowView;
     tickSpacing = undefined;
@@ -292,6 +292,7 @@ const DownloadBtn = withHandlers({ exportSequenceToFile })(props => {
             [
               "exportSequenceAsGenbank",
               "exportSequenceAsFasta",
+              "exportDNASequenceAsFasta",
               "exportSequenceAsTeselagenJson"
             ],
             [

diff --git a/packages/ove/src/ToolBar/downloadTool.js b/packages/ove/src/ToolBar/downloadTool.js
@@ -29,6 +29,7 @@ const Dropdown = withEditorProps(props => {
         [
           "exportSequenceAsGenbank",
           "exportSequenceAsFasta",
+          "exportDNASequenceAsFasta",
           "exportSequenceAsTeselagenJson"
         ],
         getCommands({ props })

diff --git a/packages/ove/src/commands/index.js b/packages/ove/src/commands/index.js
@@ -268,6 +268,11 @@ const fileCommandDefs = {
     name: "Download FASTA File",
     handler: props => props.exportSequenceToFile("fasta")
   },
+  exportDNASequenceAsFasta: {
+    name: "Download DNA FASTA File",
+    isHidden: props => !isProtein(props) || !props.sequenceData.sequence,
+    handler: props => props.exportSequenceToFile("fasta", { useDNA: true })
+  },
   exportSequenceAsTeselagenJson: {
     name: "Download Teselagen JSON File",
     handler: props => props.exportSequenceToFile("teselagenJson")

diff --git a/packages/ove/src/withEditorProps/index.js b/packages/ove/src/withEditorProps/index.js
@@ -50,8 +50,8 @@ const getUpperOrLowerSeq = defaultMemoize(
     uppercaseSequenceMapFont === "uppercase"
       ? sequence.toUpperCase()
       : uppercaseSequenceMapFont === "lowercase"
-      ? sequence.toLowerCase()
-      : sequence
+        ? sequence.toLowerCase()
+        : sequence
 );
 
 const getTypesToOmit = annotationsToSupport => {
@@ -284,7 +284,7 @@ export const importSequenceFromFile =
     }
   };
 
-export const exportSequenceToFile = props => format => {
+export const exportSequenceToFile = props => (format, options) => {
   const { sequenceData } = props;
   let convert, fileExt;
 
@@ -304,7 +304,9 @@ export const exportSequenceToFile = props => format => {
     console.error(`Invalid export format: '${format}'`); // dev error
     return;
   }
-  const blob = new Blob([convert(sequenceData)], { type: "text/plain" });
+  const blob = new Blob([convert(sequenceData, options)], {
+    type: "text/plain"
+  });
   const filename = `${sequenceData.name || "Untitled_Sequence"}.${fileExt}`;
   FileSaver.saveAs(blob, filename);
   window.toastr.success("File Downloaded Successfully");
@@ -441,16 +443,16 @@ export default compose(
             selectionLayer.start > -1
               ? { ...selectionLayer, id: undefined }
               : caretPosition > -1
-              ? {
-                  start: caretPosition,
-                  end: sequenceData.isProtein
-                    ? caretPosition + 2
-                    : caretPosition
-                }
-              : {
-                  start: 0,
-                  end: sequenceData.isProtein ? 2 : 0
-                };
+                ? {
+                    start: caretPosition,
+                    end: sequenceData.isProtein
+                      ? caretPosition + 2
+                      : caretPosition
+                  }
+                : {
+                    start: 0,
+                    end: sequenceData.isProtein ? 2 : 0
+                  };
           showAddOrEditAnnotationDialog({
             type: key.toLowerCase(),
             annotation: {