adding computeDigestFragments and getDigestFragsForSeqAndEnzymes func…

…tions
TeselaGen · Sep 7, 2022 · 7c15d45 · 7c15d45
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Showing 11 changed files with 212 additions and 11,454 deletions.
diff --git a/src/computeDigestFragments.js b/src/computeDigestFragments.js
@@ -0,0 +1,151 @@
+const { flatMap, cloneDeep } = require("lodash");
+const bsonObjectId = require("bson-objectid");
+
+const {
+  normalizePositionByRangeLength,
+  getRangeLength
+} = require("ve-range-utils");
+const getCutsitesFromSequence = require("./getCutsitesFromSequence");
+
+function computeDigestFragments({
+  cutsites,
+  sequenceLength,
+  circular,
+  //optional:
+  computePartialDigest,
+  computeDigestDisabled,
+  computePartialDigestDisabled,
+  selectionLayerUpdate,
+  updateSelectedFragment
+}) {
+  const fragments = [];
+  const overlappingEnzymes = [];
+  const pairs = [];
+
+  const sortedCutsites = cutsites.sort((a, b) => {
+    return a.topSnipPosition - b.topSnipPosition;
+  });
+  if (!circular) {
+    sortedCutsites.push({
+      id: "seqTerm_" + bsonObjectId().str,
+      start: 0,
+      end: 0,
+      overhangBps: "",
+      topSnipPosition: 0,
+      bottomSnipPosition: 0,
+      upstreamTopSnip: 0,
+      upstreamBottomSnip: 0,
+      upstreamTopBeforeBottom: false,
+      topSnipBeforeBottom: false,
+      recognitionSiteRange: {
+        start: 0,
+        end: 0
+      },
+      forward: true,
+      name: "Sequence_Terminus",
+      restrictionEnzyme: {
+        name: "Sequence_Terminus"
+      }
+    });
+  }
+
+  sortedCutsites.forEach((cutsite1, index) => {
+    if (computePartialDigest && !computePartialDigestDisabled) {
+      sortedCutsites.forEach((cs, index2) => {
+        if (index2 === index + 1 || index2 === 0) {
+          return;
+        }
+        pairs.push([cutsite1, sortedCutsites[index2]]);
+      });
+    }
+    if (!computeDigestDisabled) {
+      pairs.push([
+        cutsite1,
+        sortedCutsites[index + 1]
+          ? sortedCutsites[index + 1]
+          : sortedCutsites[0]
+      ]);
+    }
+  });
+
+  pairs.forEach(r => {
+    let [cut1, cut2] = r;
+
+    const start = normalizePositionByRangeLength(
+      cut1.topSnipPosition,
+      sequenceLength
+    );
+    const end = normalizePositionByRangeLength(
+      cut2.topSnipPosition - 1,
+      sequenceLength
+    );
+    const size = getRangeLength({ start, end }, sequenceLength);
+
+    // const id = uniqid()
+    let isFormedFromLinearEnd;
+    if (cut1.name === "Sequence_Terminus") {
+      cut1 = cloneDeep(cut1);
+      isFormedFromLinearEnd = true;
+      cut1.name = "Linear_Sequence_Start";
+      cut1.restrictionEnzyme.name = "Linear_Sequence_Start";
+    } else if (cut2.name === "Sequence_Terminus") {
+      cut2 = cloneDeep(cut2);
+      isFormedFromLinearEnd = true;
+      cut2.name = "Linear_Sequence_End";
+      cut2.restrictionEnzyme.name = "Linear_Sequence_End";
+    }
+
+    const id = start + "-" + end + "-" + size + "-";
+    const name = `${cut1.restrictionEnzyme.name} -- ${cut2.restrictionEnzyme.name} ${size} bps`;
+    getRangeLength({ start, end }, sequenceLength);
+
+    fragments.push({
+      isFormedFromLinearEnd,
+      madeFromOneCutsite: cut1 === cut2,
+      start,
+      end,
+      size,
+      id,
+      name,
+      cut1,
+      cut2,
+      onFragmentSelect:
+        selectionLayerUpdate && updateSelectedFragment
+          ? () => {
+              selectionLayerUpdate({
+                start,
+                end,
+                name
+              });
+
+              updateSelectedFragment(id);
+            }
+          : undefined
+    });
+  });
+  fragments.filter(fragment => {
+    if (!fragment.size) {
+      overlappingEnzymes.push(fragment);
+      return false;
+    }
+    return true;
+  });
+  return {
+    computePartialDigestDisabled,
+    computeDigestDisabled,
+    fragments,
+    overlappingEnzymes
+  };
+}
+
+function getDigestFragsForSeqAndEnzymes({ sequence, circular, enzymes }) {
+  const cutsitesByName = getCutsitesFromSequence(sequence, circular, enzymes);
+  return computeDigestFragments({
+    cutsites: flatMap(cutsitesByName),
+    sequenceLength: sequence.length,
+    circular
+  });
+}
+
+module.exports.computeDigestFragments = computeDigestFragments;
+module.exports.getDigestFragsForSeqAndEnzymes = getDigestFragsForSeqAndEnzymes;
diff --git a/src/computeDigestFragments.test.js b/src/computeDigestFragments.test.js
@@ -0,0 +1,44 @@
+const {
+  getDigestFragsForSeqAndEnzymes
+} = require("./computeDigestFragments.js");
+const aliasedEnzymesByName = require("./aliasedEnzymesByName");
+
+describe("computeDigestFragments", function() {
+  it.only("it should correctly generate fragments for bamhi cutting once in a circular sequence", function() {
+    const result = getDigestFragsForSeqAndEnzymes({
+      sequence: "ggggatccggggggggggggggggggggggggggggggggggggggggg",
+      circular: true,
+      enzymes: [aliasedEnzymesByName.bamhi]
+    });
+    expect(result.fragments).toHaveLength(1);
+    expect(result.fragments[0].start).toEqual(3);
+    expect(result.fragments[0].end).toEqual(2);
+    expect(result.fragments[0].size).toEqual(49);
+    expect(result.fragments[0].madeFromOneCutsite).toEqual(true);
+  });
+  it("it should correctly generate fragments for bamhi cutting once in a linear sequence", function() {
+    const result = getDigestFragsForSeqAndEnzymes({
+      sequence: "ggggatccggggggggggggggggggggggggggggggggggggggggg",
+      circular: false,
+      enzymes: [aliasedEnzymesByName.bamhi]
+    });
+    expect(result.fragments).toHaveLength(2);
+    expect(result.fragments[0].isFormedFromLinearEnd).toEqual(true);
+    expect(result.fragments[0].name).toEqual(
+      "BamHI -- Linear_Sequence_End 46 bps"
+    );
+    expect(result.fragments[0].start).toEqual(3);
+    expect(result.fragments[0].end).toEqual(48);
+    expect(result.fragments[0].size).toEqual(46);
+    expect(result.fragments[0].madeFromOneCutsite).toEqual(false);
+
+    expect(result.fragments[1].isFormedFromLinearEnd).toEqual(true);
+    expect(result.fragments[1].name).toEqual(
+      "Linear_Sequence_Start -- BamHI 3 bps"
+    );
+    expect(result.fragments[1].start).toEqual(0);
+    expect(result.fragments[1].end).toEqual(2);
+    expect(result.fragments[1].size).toEqual(3);
+    expect(result.fragments[1].madeFromOneCutsite).toEqual(false);
+  });
+});
diff --git a/src/cutSequenceByRestrictionEnzyme.js b/src/cutSequenceByRestrictionEnzyme.js
@@ -1,4 +1,6 @@
 const { assign } = require("lodash");
+const bsonObjectId = require("bson-objectid");
+
 const getReverseComplementSequenceString = require("./getReverseComplementSequenceString");
 
 const {
@@ -12,19 +14,6 @@ module.exports = function cutSequenceByRestrictionEnzyme(
   circular,
   restrictionEnzyme
 ) {
-  // ac.throw([
-  //     ac.string,
-  //     ac.bool,
-  //     ac.shape({
-  //         "name": ac.string,
-  //         "site": ac.string,
-  //         "forwardRegex": ac.string,
-  //         "reverseRegex": ac.string,
-  //         "cutsTwice": ac.number,
-  //         "topSnipOffset": ac.number,
-  //         "bottomSnipOffset": ac.number
-  //     })
-  // ], arguments);
   if (
     restrictionEnzyme.forwardRegex.length === 0 ||
     restrictionEnzyme.reverseRegex.length === 0
@@ -280,6 +269,7 @@ function cutSequence(
       let overhangBps = getSequenceWithinRange(cutRange, originalSequence);
 
       restrictionCutSite = {
+        id: bsonObjectId().str,
         start,
         end,
         topSnipPosition,

diff --git a/src/generateSequenceData.js b/src/generateSequenceData.js
@@ -2,7 +2,7 @@
 
 // var ac = require('ve-api-check');
 const { generateRandomRange } = require("ve-range-utils");
-const objectid = require("bson-objectid");
+const bsonObjectId = require("bson-objectid");
 
 module.exports = function generateSequenceData({
   isProtein,
@@ -83,7 +83,7 @@ function generateAnnotation(start, end, maxLength) {
     ...range,
     name: getRandomInt(0, 100000).toString(),
     type: "misc_feature",
-    id: objectid().str,
+    id: bsonObjectId().str,
     forward: Math.random() > 0.5,
     notes: {}
   };

diff --git a/src/getCutsitesFromSequence.js b/src/getCutsitesFromSequence.js
@@ -1,20 +1,11 @@
-// const ac = require('ve-api-check');
 const cutSequenceByRestrictionEnzyme = require("./cutSequenceByRestrictionEnzyme");
 
 module.exports = function getCutsitesFromSequence(
   sequence,
   circular,
   restrictionEnzymes
 ) {
-  //validate args!
-  // ac.throw([
-  //     ac.string,
-  //     ac.bool,
-  //     ac.array
-  // ], arguments);
-
   const cutsitesByName = {};
-  // const allCutsite= [];
   for (let i = 0; i < restrictionEnzymes.length; i++) {
     const re = restrictionEnzymes[i];
     const cutsites = cutSequenceByRestrictionEnzyme(sequence, circular, re);

diff --git a/src/getOrfsFromSequence.js b/src/getOrfsFromSequence.js
@@ -1,4 +1,4 @@
-const ObjectId = require("bson-objectid");
+const bsonObjectId = require("bson-objectid");
 const getReverseComplementSequenceString = require("./getReverseComplementSequenceString");
 // const ac = require('ve-api-check');
 /**
@@ -73,7 +73,7 @@ module.exports = function getOrfsFromSequence(options) {
           forward: forward,
           annotationTypePlural: "orfs",
           isOrf: true,
-          id: ObjectId().str
+          id: bsonObjectId().str
         });
       }
     }

diff --git a/src/index.js b/src/index.js
@@ -42,6 +42,8 @@ module.exports.getComplementSequenceAndAnnotations = require("./getComplementSeq
 module.exports.getComplementSequenceString = require("./getComplementSequenceString");
 module.exports.getCutsitesFromSequence = require("./getCutsitesFromSequence");
 module.exports.getCutsiteType = require("./getCutsiteType");
+module.exports.computeDigestFragments = require("./computeDigestFragments").computeDigestFragments;
+module.exports.getDigestFragsForSeqAndEnzymes = require("./computeDigestFragments").getDigestFragsForSeqAndEnzymes;
 module.exports.getInsertBetweenVals = require("./getInsertBetweenVals");
 module.exports.getLeftAndRightOfSequenceInRangeGivenPosition = require("./getLeftAndRightOfSequenceInRangeGivenPosition");
 module.exports.getOrfsFromSequence = require("./getOrfsFromSequence");

diff --git a/src/tidyUpAnnotation.js b/src/tidyUpAnnotation.js
@@ -1,7 +1,7 @@
 const { cloneDeep, get } = require("lodash");
 const FeatureTypes = require("./FeatureTypes.js");
 const featureColors = require("./featureColors");
-const bsonObjectid = require("bson-objectid");
+const bsonObjectId = require("bson-objectid");
 
 module.exports = function tidyUpAnnotation(
   _annotation,
@@ -34,10 +34,10 @@ module.exports = function tidyUpAnnotation(
     annotation.name = "Untitled annotation";
   }
   if (provideNewIdsForAnnotations) {
-    annotation.id = bsonObjectid().str;
+    annotation.id = bsonObjectId().str;
   }
   if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-    annotation.id = bsonObjectid().str;
+    annotation.id = bsonObjectId().str;
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id
     );

diff --git a/src/tidyUpSequenceData.js b/src/tidyUpSequenceData.js
@@ -1,5 +1,5 @@
 // tnrtodo: figure out where to insert this validation exactly..
-const bsonObjectid = require("bson-objectid");
+const bsonObjectId = require("bson-objectid");
 const getAminoAcidDataForEachBaseOfDna = require("./getAminoAcidDataForEachBaseOfDna");
 const { cloneDeep, flatMap } = require("lodash");
 const annotationTypes = require("./annotationTypes");
@@ -148,7 +148,7 @@ module.exports = function tidyUpSequenceData(pSeqData, options = {}) {
         if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
-          itemId = bsonObjectid().str;
+          itemId = bsonObjectId().str;
           if (!doNotProvideIdsForAnnotations) {
             item.id = itemId; //assign the newly created id to the item
           }