@teselagen/bio-parsers 0.3.8 → 0.3.9

package/src/utils/constants.js

@@ -1,24 +1,24 @@
-export const untitledSequenceName = 'Untitled Sequence';
+export const untitledSequenceName = "Untitled Sequence";
 
 export const gbDivisions = {
-    // https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#GenBankDivisionB
-    PRI: true,  //- primate sequences
-    ROD: true,  //- rodent sequences
-    MAM: true,  //- other mammalian sequences
-    VRT: true,  //- other vertebrate sequences
-    INV: true,  //- invertebrate sequences
-    PLN: true,  //- plant, fungal, and algal sequences
-    BCT: true,  //- bacterial sequences
-    VRL: true,  //- viral sequences
-    PHG: true,  //- bacteriophage sequences
-    SYN: true,  //- synthetic sequences
-    UNA: true,  //- unannotated sequences
-    EST: true,  //- EST sequences (expressed sequence tags)
-    PAT: true,  //- patent sequences
-    STS: true,  //- STS sequences (sequence tagged sites)
-    GSS: true,  //- GSS sequences (genome survey sequences)
-    HTG: true,  //- HTG sequences (high-throughput genomic sequences)
-    HTC: true,  //- unfinished high-throughput cDNA sequencing
-    ENV: true,  //- environmental sampling sequences
-    CON: true,  //- sequence assembly instructions on how to construct contigs from multiple GenBank records.
-  }
+  // https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#GenBankDivisionB
+  PRI: true, //- primate sequences
+  ROD: true, //- rodent sequences
+  MAM: true, //- other mammalian sequences
+  VRT: true, //- other vertebrate sequences
+  INV: true, //- invertebrate sequences
+  PLN: true, //- plant, fungal, and algal sequences
+  BCT: true, //- bacterial sequences
+  VRL: true, //- viral sequences
+  PHG: true, //- bacteriophage sequences
+  SYN: true, //- synthetic sequences
+  UNA: true, //- unannotated sequences
+  EST: true, //- EST sequences (expressed sequence tags)
+  PAT: true, //- patent sequences
+  STS: true, //- STS sequences (sequence tagged sites)
+  GSS: true, //- GSS sequences (genome survey sequences)
+  HTG: true, //- HTG sequences (high-throughput genomic sequences)
+  HTC: true, //- unfinished high-throughput cDNA sequencing
+  ENV: true, //- environmental sampling sequences
+  CON: true //- sequence assembly instructions on how to construct contigs from multiple GenBank records.
+};

package/src/utils/convertOldSequenceDataToNewDataType.js

@@ -1,4 +1,4 @@
-import { isRangeWithinRange } from '@teselagen/range-utils';
+import { isRangeWithinRange } from "@teselagen/range-utils";
 
 export default function convertOldSequenceDataToNewDataType(
   oldTeselagenJson,
@@ -7,7 +7,7 @@ export default function convertOldSequenceDataToNewDataType(
   if (opts && opts.splitLocations) {
     //after the file has been parsed, but before it's been saved, check for features with multiple locations and split them
     oldTeselagenJson &&
-      oldTeselagenJson.features.forEach(function(feature) {
+      oldTeselagenJson.features.forEach(function (feature) {
         if (feature.locations && feature.locations[0]) {
           if (feature.locations.length > 1) {
             for (let i = 1; i < feature.locations.length; i++) {
@@ -31,11 +31,10 @@ export default function convertOldSequenceDataToNewDataType(
         }
         delete feature.locations;
       });
-
   } else {
     //mange locations
     oldTeselagenJson &&
-      oldTeselagenJson.features.forEach(function(feature) {
+      oldTeselagenJson.features.forEach(function (feature) {
         if (feature.locations && feature.locations[0]) {
           //set the new starts and ends
           feature.start = feature.locations[0].start;
@@ -53,7 +52,7 @@ export default function convertOldSequenceDataToNewDataType(
               delete feature.locations;
             }
           } else {
-            delete feature.locations
+            delete feature.locations;
           }
         }
       });
@@ -61,4 +60,4 @@ export default function convertOldSequenceDataToNewDataType(
   if (Array.isArray(oldTeselagenJson.sequence)) {
     oldTeselagenJson.sequence = oldTeselagenJson.sequence.join("");
   }
-};
+}

package/src/utils/createInitialSequence.js

@@ -1,14 +1,16 @@
 import { untitledSequenceName } from "./constants";
 
 export default function createInitialSequence(options) {
-    options = options || {}
-    return {
-        messages: [],
-        success: true,
-        parsedSequence: {
-            features: [],
-            name: (options.fileName && options.fileName.replace(/\.[^/.]+$/, "")) || untitledSequenceName,
-            sequence: ''
-        }
-    };
-};
+  options = options || {};
+  return {
+    messages: [],
+    success: true,
+    parsedSequence: {
+      features: [],
+      name:
+        (options.fileName && options.fileName.replace(/\.[^/.]+$/, "")) ||
+        untitledSequenceName,
+      sequence: ""
+    }
+  };
+}

package/src/utils/extractFileExtension.js

@@ -1,14 +1,12 @@
 export default function extractFileExtension(name) {
-	if (typeof name === 'string') {
-		let ext = "";
-		const match = name.match(/\.(\w+)$/);
-		if (match && match[1]) {
-			ext = match[1];
-		}
-		return ext;
-	}
-	else {
-		return "";
-	}
-};
-
+  if (typeof name === "string") {
+    let ext = "";
+    const match = name.match(/\.(\w+)$/);
+    if (match && match[1]) {
+      ext = match[1];
+    }
+    return ext;
+  } else {
+    return "";
+  }
+}

package/src/utils/flattenSequenceArray.js

@@ -1,17 +1,17 @@
-import convertOldSequenceDataToNewDataType from './convertOldSequenceDataToNewDataType.js';
+import convertOldSequenceDataToNewDataType from "./convertOldSequenceDataToNewDataType.js";
 
 export default function flattenSequenceArray(parsingResultArray, opts) {
-    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) {
-                convertOldSequenceDataToNewDataType(parsingResult.parsedSequence, opts);
-            }
-        });
+  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) {
+        convertOldSequenceDataToNewDataType(parsingResult.parsedSequence, opts);
+      }
+    });
+  }
+  return parsingResultArray;
+}

package/src/utils/getArrayBufferFromFile.js

@@ -1,5 +1,5 @@
-import { Buffer } from 'buffer';
-import isBrowser from './isBrowser';
+import { Buffer } from "buffer";
+import isBrowser from "./isBrowser";
 
 export default function getArrayBufferFromFile(file) {
   if (!isBrowser) {
@@ -9,11 +9,11 @@ export default function getArrayBufferFromFile(file) {
 
   const reader = new window.FileReader();
   return new Promise((resolve, reject) => {
-    reader.onload = (e) => {
+    reader.onload = e => {
       resolve(e.target.result);
     };
-    reader.onerror = (err) => {
-      console.error('err:', err);
+    reader.onerror = err => {
+      console.error("err:", err);
       reject(err);
     };
     reader.readAsArrayBuffer(

package/src/utils/isBrowser.js

@@ -1 +1,2 @@
-export default typeof window !== 'undefined' && typeof window.document !== 'undefined';
+export default typeof window !== "undefined" &&
+  typeof window.document !== "undefined";

package/src/utils/parseUracilFeatures.js

@@ -5,9 +5,9 @@ export default function parseUracilFeatures(sequenceBps, featureList = []) {
       name: "tg_uracil",
       strand: 1,
       start: index,
-      end: index,
+      end: index
     });
     return u === "U" ? "T" : "t";
   });
-  return cleanedBps
+  return cleanedBps;
 }

package/src/utils/pragmasAndTypes.js

@@ -1,5 +1,6 @@
 export default [
-  { //primers don't need a pragma because they already have a feature type of primer_bind
+  {
+    //primers don't need a pragma because they already have a feature type of primer_bind
     type: "primers"
   },
   {
@@ -18,4 +19,4 @@ export default [
     pragma: "j5_lineage_annotation",
     type: "lineageAnnotations"
   }
-]
+];

package/src/utils/searchWholeObjByName.js

@@ -16,7 +16,7 @@ class Match {
   logValue() {
     const val = this.value;
     // if value is an object then just toString it
-    const isPrimitive = (x) => Object(x) !== x;
+    const isPrimitive = x => Object(x) !== x;
     return isPrimitive(val) || Array.isArray(val) ? val : {}.toString.call(val);
   }
 
@@ -39,7 +39,7 @@ export default function searchWholeObjByName(what, where) {
 
   const matches = [];
   matches.log = function () {
-    this.forEach((m) => m.log());
+    this.forEach(m => m.log());
   };
 
   // a non-recursive solution to avoid call stack limits
@@ -77,7 +77,7 @@ export default function searchWholeObjByName(what, where) {
               path: `${path}.${prop}`,
               obj: where,
               prop,
-              type,
+              type
             });
             matches.push(match);
           }

package/src/utils/splitStringIntoLines.js

@@ -1,13 +1,14 @@
 export default function splitStringIntoLines(string) {
-	let lines = [];
-	if (string === "") {
-		return lines;
-	}
-	else {
-		lines = string.split(/\r?\n/);
-		if (lines.length == 1) { //tnr: not sure why this check is being made... but keeping it in because it is probably doing something
-			lines = string.split('\\n');
-		}
-		return lines;
-	}
-};
+  let lines = [];
+  if (string === "") {
+    return lines;
+  } else {
+    lines = string.split(/\r?\n/);
+    // eslint-disable-next-line eqeqeq
+    if (lines.length == 1) {
+      //tnr: not sure why this check is being made... but keeping it in because it is probably doing something
+      lines = string.split("\\n");
+    }
+    return lines;
+  }
+}

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];
     }
@@ -110,7 +110,7 @@ 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"
       );
     }
@@ -299,16 +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" &&
@@ -317,7 +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;
@@ -333,7 +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;
@@ -344,7 +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
@@ -356,7 +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;