@datagrok-libraries/bio 5.36.0 → 5.37.0

package/CHANGELOG.md

@@ -1,5 +1,18 @@
 # bio changelog
 
+## 5.37.0 (2023-08-30)
+
+### Features
+
+* Added `calculateSimilarity` and `calculateIdentity` functions.
+* Added `calculateScores` function.
+
+## 5.36.1 (2023-08-18)
+
+### Bug fixes
+
+* Restore utils `getSplitter` method, it is required for MacromoleculeDifference column.
+
 ## 5.36.0 (2023-08-10)
 
 This release introduces chemical sequence similarity functionality.

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.36.0",
+  "version": "5.37.0",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.64",

package/src/utils/macromolecule/scoring.d.ts

@@ -0,0 +1,24 @@
+import { ISeqSplitted } from '../../utils/macromolecule/types';
+import * as DG from 'datagrok-api/dg';
+export declare enum SCORE {
+    IDENTITY = "identity",
+    SIMILARITY = "similarity"
+}
+/** Performs transformations and sequence scoring.
+ * @param {DG.DataFrame} table Table to attach results to.
+ * @param {DG.Column<string>} col Sequences column to score. Must have Macromolecule semantic type.
+ * @param {string} ref Reference sequence to score against.
+ * @param {SCORE} scoring Scoring method.
+ * @returns {DG.Column<number>} Scores column. */
+export declare function calculateScores(table: DG.DataFrame, col: DG.Column<string>, ref: string, scoring: SCORE): Promise<DG.Column<number>>;
+/** Calculates identity scores as fraction of matching monomers on the same position.
+ * @param {ISeqSplitted} reference Splitted reference sequence.
+ * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
+ * @returns {DG.Column<number>} Scores column. */
+export declare function calculateIdentity(reference: ISeqSplitted, positionsDf: DG.DataFrame): DG.Column<number>;
+/** Calculates similarity scores as sum of monomer fingerprint similarities on the same position.
+ * @param {ISeqSplitted} reference Splitted reference sequence.
+ * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
+ * @returns {DG.Column<number>} Scores column. */
+export declare function calculateSimilarity(reference: ISeqSplitted, positionsDf: DG.DataFrame): Promise<DG.Column<number>>;
+//# sourceMappingURL=scoring.d.ts.map

package/src/utils/macromolecule/scoring.d.ts.map

@@ -0,0 +1 @@
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package/src/utils/macromolecule/scoring.js

@@ -0,0 +1,65 @@
+import { sequenceChemSimilarity } from '../../monomer-works/monomer-utils';
+import * as DG from 'datagrok-api/dg';
+import { splitAlignedSequences } from '../splitter';
+import { getSplitter } from './utils';
+export var SCORE;
+(function (SCORE) {
+    SCORE["IDENTITY"] = "identity";
+    SCORE["SIMILARITY"] = "similarity";
+})(SCORE || (SCORE = {}));
+/** Performs transformations and sequence scoring.
+ * @param {DG.DataFrame} table Table to attach results to.
+ * @param {DG.Column<string>} col Sequences column to score. Must have Macromolecule semantic type.
+ * @param {string} ref Reference sequence to score against.
+ * @param {SCORE} scoring Scoring method.
+ * @returns {DG.Column<number>} Scores column. */
+export async function calculateScores(table, col, ref, scoring) {
+    const splitSeqDf = splitAlignedSequences(col);
+    const splitter = getSplitter(col.getTag(DG.TAGS.UNITS), col.getTag("separator" /* bioTAGS.separator */));
+    const refSplitted = splitter(ref);
+    const scoresCol = scoring === SCORE.IDENTITY ? calculateIdentity(refSplitted, splitSeqDf) :
+        scoring === SCORE.SIMILARITY ? await calculateSimilarity(refSplitted, splitSeqDf) : null;
+    if (scoresCol === null)
+        throw new Error(`In bio library: Unkown sequence scoring method: ${scoring}`);
+    scoresCol.name = table.columns.getUnusedName(scoresCol.name);
+    table.columns.add(scoresCol);
+    return scoresCol;
+}
+/** Calculates identity scores as fraction of matching monomers on the same position.
+ * @param {ISeqSplitted} reference Splitted reference sequence.
+ * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
+ * @returns {DG.Column<number>} Scores column. */
+export function calculateIdentity(reference, positionsDf) {
+    const numPositions = positionsDf.columns.length;
+    const positionCols = new Array(numPositions);
+    const positionEmptyCategories = new Array(numPositions);
+    const categoryIndexesTemplate = new Array(numPositions);
+    for (let posIdx = 0; posIdx < numPositions; ++posIdx) {
+        const posCol = positionsDf.columns.byIndex(posIdx);
+        positionCols[posIdx] = posCol.getRawData();
+        positionEmptyCategories[posIdx] = posCol.categories.indexOf('');
+        categoryIndexesTemplate[posIdx] = posCol.categories.indexOf(reference[posIdx] ?? '');
+    }
+    const identityScoresCol = DG.Column.float('Identity', positionsDf.rowCount);
+    const identityScoresData = identityScoresCol.getRawData();
+    for (let rowIndex = 0; rowIndex < positionsDf.rowCount; ++rowIndex) {
+        identityScoresData[rowIndex] = 0;
+        for (let posIdx = 0; posIdx < reference.length; ++posIdx) {
+            const categoryIndex = positionCols[posIdx][rowIndex];
+            if (categoryIndex === categoryIndexesTemplate[posIdx])
+                ++identityScoresData[rowIndex];
+        }
+        identityScoresData[rowIndex] /= reference.length;
+    }
+    return identityScoresCol;
+}
+/** Calculates similarity scores as sum of monomer fingerprint similarities on the same position.
+ * @param {ISeqSplitted} reference Splitted reference sequence.
+ * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
+ * @returns {DG.Column<number>} Scores column. */
+export async function calculateSimilarity(reference, positionsDf) {
+    const monomerColumns = positionsDf.columns.toList();
+    const scoresCol = await sequenceChemSimilarity(monomerColumns, reference);
+    return scoresCol;
+}
+//# sourceMappingURL=scoring.js.map

package/src/utils/macromolecule/scoring.js.map

@@ -0,0 +1 @@
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package/src/utils/macromolecule/utils.d.ts

@@ -29,6 +29,13 @@ export declare function getSplitterWithSeparator(separator: string, limit?: numb
 export declare function splitterAsHelm(seq: any): string[];
 /** Func type to shorten a {@link monomerLabel} with length {@link limit} */
 export type MonomerToShortFunc = (monomerLabel: string, limit: number) => string;
+/** Get splitter method to split sequences to monomers (required for MacromoleculeDifferenceCellRenderer)
+ * @param {string} units
+ * @param {string} separator
+ * @param limit
+ * @return {SplitterFunc}
+ */
+export declare function getSplitter(units: string, separator: string, limit?: number | undefined): SplitterFunc;
 /** Generate splitter function for sequence column
  * @param {DG.Column} col
  * @return {SplitterFunc} Splitter function

package/src/utils/macromolecule/utils.d.ts.map

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package/src/utils/macromolecule/utils.js

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { CandidateSimType } from './types';
-import { Alphabets, candidateAlphabets, monomerRe } from './consts';
+import { Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
 import { UnitsHandler } from '../units-handler';
 import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
 import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
@@ -92,6 +92,23 @@ export function splitterAsHelm(seq) {
     const mmList = inSeq ? inSeq.split('.') : [];
     return mmList.map(mmPostProcess);
 }
+/** Get splitter method to split sequences to monomers (required for MacromoleculeDifferenceCellRenderer)
+ * @param {string} units
+ * @param {string} separator
+ * @param limit
+ * @return {SplitterFunc}
+ */
+export function getSplitter(units, separator, limit = undefined) {
+    if (units.toLowerCase().startsWith(NOTATION.FASTA))
+        return splitterAsFasta;
+    else if (units.toLowerCase().startsWith(NOTATION.SEPARATOR))
+        return getSplitterWithSeparator(separator, limit);
+    else if (units.toLowerCase().startsWith(NOTATION.HELM))
+        return splitterAsHelm;
+    else
+        throw new Error(`Unexpected units ${units} .`);
+    // TODO: Splitter for HELM
+}
 /** Generate splitter function for sequence column
  * @param {DG.Column} col
  * @return {SplitterFunc} Splitter function

package/src/utils/macromolecule/utils.js.map

@@ -1 +1 @@
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package/src/viewers/web-logo.d.ts

@@ -11,11 +11,13 @@ export declare enum PositionHeight {
     Entropy = "Entropy",
     full = "100%"
 }
+/** top, middle, bottom */
 export declare enum VerticalAlignments {
     TOP = "top",
     MIDDLE = "middle",
     BOTTOM = "bottom"
 }
+/** left, center, right */
 export declare enum HorizontalAlignments {
     LEFT = "left",
     CENTER = "center",

package/src/viewers/web-logo.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"web-logo.d.ts","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAEjC,oBAAY,IAAI;IACd,aAAa,sBAAsB;IACnC,cAAc,uBAAuB;IAErC,6EAA6E;IAC7E,cAAc,oBAAoB;CACnC;AAED,oBAAY,cAAc;IACxB,OAAO,YAAY;IACnB,IAAI,SAAS;CACd;AAED,oBAAY,kBAAkB;IAC5B,GAAG,QAAQ;IACX,MAAM,WAAW;IACjB,MAAM,WAAW;CAClB;AAED,oBAAY,oBAAoB;IAC9B,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,KAAK,UAAU;CAChB;AAED,oBAAY,oBAAoB;IAC9B,IAAI,SAAS;IACb,EAAE,OAAO;IACT,GAAG,QAAQ;CACZ;AAED,qEAAqE;AACrE,oBAAY,aAAa;IACvB,0DAA0D;IAC1D,QAAQ,aAAa;IACrB,oFAAoF;IACpF,QAAQ,aAAa;CACtB;AAED,eAAO,MAAM,mBAAmB;wBAEV,MAAM,GAAG,IAAI;uBACd,MAAM,GAAG,IAAI;qBACf,MAAM,GAAG,IAAI;wBACV,OAAO;wBACP,OAAO;qBACV,OAAO;qBAGP,MAAM;oBACP,MAAM;mBACP,MAAM;uBAGF,kBAAkB;yBAChB,oBAAoB;cAC/B,OAAO;aACR,OAAO;eACL,MAAM;eACN,MAAM;wBACG,OAAO;yBACN,oBAAoB;oBACzB,MAAM;kBAGR,aAAa;CAC1B,CAAC;AAEJ,MAAM,MAAM,YAAY,GAAG,QAAQ,CAAC,OAAO,mBAAmB,CAAC,CAAC;AAEhE,MAAM,WAAW,cAAe,SAAQ,YAAY,EAAE,OAAO;IAC3D,IAAI,aAAa,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC;IAEtC,UAAU,CAAC,OAAO,EAAE,OAAO,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC;CAClD;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAC9C,eAAO,MAAM,UAAU,EAAE,MAAwB,CAAC;AAElD,OAAO,QAAQ,iBAAiB,CAAC;IAC/B,UAAiB,mBAAmB;QAClC,QAAQ,CAAC,UAAU,EAAE,SAAS,EAAE,OAAO,EAAE,OAAO,CAAC,YAAY,CAAC,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,GAAG,cAAc,CAAC,CAAC;KACtG;CACF"}
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package/src/viewers/web-logo.js

@@ -10,12 +10,14 @@ export var PositionHeight;
     PositionHeight["Entropy"] = "Entropy";
     PositionHeight["full"] = "100%";
 })(PositionHeight || (PositionHeight = {}));
+/** top, middle, bottom */
 export var VerticalAlignments;
 (function (VerticalAlignments) {
     VerticalAlignments["TOP"] = "top";
     VerticalAlignments["MIDDLE"] = "middle";
     VerticalAlignments["BOTTOM"] = "bottom";
 })(VerticalAlignments || (VerticalAlignments = {}));
+/** left, center, right */
 export var HorizontalAlignments;
 (function (HorizontalAlignments) {
     HorizontalAlignments["LEFT"] = "left";

package/src/viewers/web-logo.js.map

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