@teselagen/bio-parsers 0.3.7 → 0.3.9

package/src/utils/validateSequence.js

@@ -40,7 +40,7 @@ export default function validateSequence(sequence, options = {}) {
     "isSingleStrandedDNA",
     "isDoubleStrandedRNA",
     "isProtein"
-  ].forEach((k) => {
+  ].forEach(k => {
     if (options[k] !== undefined && sequence[k] === undefined) {
       sequence[k] = options[k];
     }
@@ -110,11 +110,16 @@ export default function validateSequence(sequence, options = {}) {
     //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) =>
+      sequence.sequence = sequence.sequence.replace(/u/gi, u =>
         u === "U" ? "T" : "t"
       );
     }
-    if (temp !== sequence.sequence && !sequence.isDNA && !sequence.isProtein && sequence.isRNA !== false) {
+    if (
+      temp !== sequence.sequence &&
+      !sequence.isDNA &&
+      !sequence.isProtein &&
+      sequence.isRNA !== false
+    ) {
       sequence.type = "RNA";
       sequence.sequence = temp;
     } else {
@@ -294,16 +299,16 @@ export default function validateSequence(sequence, options = {}) {
     }
     if (
       feature.notes.pragma &&
-      some(feature.notes.pragma, (p) => p === "overlapsSelf")
+      some(feature.notes.pragma, p => p === "overlapsSelf")
     ) {
       feature.overlapsSelf = true;
       feature.notes.pragma = filter(
         feature.notes.pragma,
-        (p) => p !== "overlapsSelf"
+        p => p !== "overlapsSelf"
       );
     }
     feature.notes.note &&
-      some(feature.notes.note, (n) => {
+      some(feature.notes.note, n => {
         if (
           n &&
           typeof n === "string" &&
@@ -312,7 +317,7 @@ export default function validateSequence(sequence, options = {}) {
           //remove it after we're parsed it out
           feature.notes.note = filter(
             feature.notes.note,
-            (p) => p && !p.toLowerCase().includes("sequence:")
+            p => p && !p.toLowerCase().includes("sequence:")
           );
           if (feature.notes.note.length === 0) {
             delete feature.notes.note;
@@ -328,7 +333,7 @@ export default function validateSequence(sequence, options = {}) {
       });
 
     feature.notes.primerBindsOn &&
-      some(feature.notes.primerBindsOn, (n) => {
+      some(feature.notes.primerBindsOn, n => {
         if (n) {
           feature.primerBindsOn = n;
           delete feature.notes.primerBindsOn;
@@ -339,7 +344,7 @@ export default function validateSequence(sequence, options = {}) {
       if (
         options[`accept${upperFirst(type)}`] !== false && //acceptParts, acceptWarnings,
         feature.notes.pragma &&
-        some(feature.notes.pragma, (p) => p === pragma)
+        some(feature.notes.pragma, p => p === pragma)
       ) {
         if (!sequence[type]) {
           sequence[type] = []; //initialize an empty array if necessary
@@ -351,7 +356,7 @@ export default function validateSequence(sequence, options = {}) {
       }
     }
     forEach(feature.notes, (noteArray, key) => {
-      feature.notes[key] = map(noteArray, (note) => {
+      feature.notes[key] = map(noteArray, note => {
         return unmangleUrls(note);
       });
     });

package/src/utils/validateSequenceArray.js

@@ -1,20 +1,20 @@
-import validateSequence from './validateSequence.js';
+import validateSequence from "./validateSequence.js";
 
 export default function validateSequenceArray(parsingResultArray, options) {
-    if (parsingResultArray) {
-        if (!Array.isArray(parsingResultArray)) {
-            //wrap the parsingResult into an array if it isn't one already
-            parsingResultArray = [parsingResultArray];
-        }
-        //should convert the old data type to the new data type (flattened sequence)
-        parsingResultArray.forEach(function(parsingResult) {
-            if (parsingResult.success) {
-                const res = validateSequence(parsingResult.parsedSequence, options);
-                //add any validation error messages to the parsed sequence results messages
-                parsingResult.messages = parsingResult.messages.concat(res.messages);
-                parsingResult.parsedSequence = res.validatedAndCleanedSequence;
-            }
-        });
+  if (parsingResultArray) {
+    if (!Array.isArray(parsingResultArray)) {
+      //wrap the parsingResult into an array if it isn't one already
+      parsingResultArray = [parsingResultArray];
     }
-    return parsingResultArray;
-};
+    //should convert the old data type to the new data type (flattened sequence)
+    parsingResultArray.forEach(function (parsingResult) {
+      if (parsingResult.success) {
+        const res = validateSequence(parsingResult.parsedSequence, options);
+        //add any validation error messages to the parsed sequence results messages
+        parsingResult.messages = parsingResult.messages.concat(res.messages);
+        parsingResult.parsedSequence = res.validatedAndCleanedSequence;
+      }
+    });
+  }
+  return parsingResultArray;
+}

package/utils/getArrayBufferFromFile.d.ts

@@ -1 +1 @@
-export default function getArrayBufferFromFile(file: any): ArrayBuffer | Promise<any>;
+export default function getArrayBufferFromFile(file: any): Promise<any> | ArrayBuffer;