@teselagen/sequence-utils 0.1.22 → 0.1.24

package/src/prepareCircularViewData.test.js

@@ -0,0 +1,196 @@
+import {expect} from "chai";
+import mapAnnotationsToRows from "./mapAnnotationsToRows.js";
+describe("prepareCircularViewData", () => {
+  it("maps overlapping annotations to rows correctly", () => {
+    const annotation1 = {
+      start: 0,
+      end: 9,
+      id: "a"
+    };
+    const annotation2 = {
+      start: 0,
+      end: 9,
+      id: "b"
+    };
+    const annotations = [annotation1, annotation2];
+    const sequenceLength = 10;
+    const bpsPerRow = 5;
+    const annotationsToRowsMap = mapAnnotationsToRows(
+      annotations,
+      sequenceLength,
+      bpsPerRow
+    );
+    expect(annotationsToRowsMap).to.deep.equal({
+      0: [
+        {
+          annotation: annotation1,
+          start: 0,
+          end: 4,
+          id: annotation1.id,
+          yOffset: 0,
+          enclosingRangeType: "beginningAndEnd"
+        },
+        {
+          start: 0,
+          end: 4,
+          id: annotation2.id,
+          yOffset: 1,
+          annotation: annotation2,
+          enclosingRangeType: "beginningAndEnd"
+        }
+      ],
+      1: [
+        {
+          annotation: annotation1,
+          start: 5,
+          end: 9,
+          id: annotation1.id,
+          yOffset: 0,
+          enclosingRangeType: "beginningAndEnd"
+        },
+        {
+          start: 5,
+          end: 9,
+          id: annotation2.id,
+          yOffset: 1,
+          annotation: annotation2,
+          enclosingRangeType: "beginningAndEnd"
+        }
+      ]
+    });
+  });
+  it("correctly calculates y-offset for annotation split by origin", () => {
+    const annotation1 = {
+      start: 7,
+      end: 9,
+      id: "a"
+    };
+    const annotation2 = {
+      start: 5,
+      end: 3,
+      id: "b"
+    };
+    const annotations = [annotation1, annotation2];
+    const sequenceLength = 10;
+    const bpsPerRow = 10;
+    const annotationsToRowsMap = mapAnnotationsToRows(
+      annotations,
+      sequenceLength,
+      bpsPerRow
+    );
+    expect(annotationsToRowsMap).to.deep.equal({
+      0: [
+        {
+          start: 7,
+          end: 9,
+          id: annotation1.id,
+          yOffset: 0,
+          annotation: annotation1,
+          enclosingRangeType: "beginningAndEnd"
+        },
+        {
+          annotation: annotation2,
+          start: 0,
+          end: 3,
+          id: annotation2.id,
+          yOffset: 1,
+          enclosingRangeType: "end"
+        },
+        {
+          annotation: annotation2,
+          start: 5,
+          end: 9,
+          id: annotation2.id,
+          yOffset: 1,
+          enclosingRangeType: "beginning"
+        }
+      ]
+    });
+  });
+  it("correctly calculates y-offset for annotation split by origin (different ordering of annotations)", () => {
+    const annotation1 = {
+      start: 5,
+      end: 3,
+      id: "a"
+    };
+    const annotation2 = {
+      start: 7,
+      end: 9,
+      id: "b"
+    };
+    const annotations = [annotation1, annotation2];
+    const sequenceLength = 10;
+    const bpsPerRow = 10;
+    const annotationsToRowsMap = mapAnnotationsToRows(
+      annotations,
+      sequenceLength,
+      bpsPerRow
+    );
+    expect(annotationsToRowsMap).to.deep.equal({
+      0: [
+        {
+          annotation: annotation1,
+          start: 0,
+          end: 3,
+          id: annotation1.id,
+          yOffset: 0,
+          enclosingRangeType: "end"
+        },
+        {
+          annotation: annotation1,
+          start: 5,
+          end: 9,
+          id: annotation1.id,
+          yOffset: 0,
+          enclosingRangeType: "beginning"
+        },
+        {
+          start: 7,
+          end: 9,
+          id: annotation2.id,
+          yOffset: 1,
+          annotation: annotation2,
+          enclosingRangeType: "beginningAndEnd"
+        }
+      ]
+    });
+  });
+
+  it("maps single annotation to rows correctly", () => {
+    const annotation1 = {
+      start: 0,
+      end: 9,
+      id: "a"
+    };
+    const annotations = [annotation1];
+    const sequenceLength = 10;
+    const bpsPerRow = 5;
+    const annotationsToRowsMap = mapAnnotationsToRows(
+      annotations,
+      sequenceLength,
+      bpsPerRow
+    );
+    expect(annotationsToRowsMap).to.deep.equal({
+      0: [
+        {
+          annotation: annotation1,
+          start: 0,
+          end: 4,
+          id: annotation1.id,
+          yOffset: 0,
+          enclosingRangeType: "beginningAndEnd"
+        }
+      ],
+      1: [
+        {
+          annotation: annotation1,
+          start: 5,
+          end: 9,
+          id: annotation1.id,
+          yOffset: 0,
+          enclosingRangeType: "beginningAndEnd"
+        }
+      ]
+    });
+  });
+});

package/src/prepareRowData.js

@@ -0,0 +1,41 @@
+
+// ac.throw([ac.posInt, ac.posInt, ac.bool], arguments);
+import mapAnnotationsToRows from "./mapAnnotationsToRows";
+
+import { annotationTypes } from "./annotationTypes";
+
+export default function prepareRowData(sequenceData, bpsPerRow) {
+  // ac.throw([ac.sequenceData, ac.posInt], arguments);
+  const sequenceLength = sequenceData.sequence.length;
+  const totalRows = Math.ceil(sequenceLength / bpsPerRow) || 1; //this check makes sure there is always at least 1 row!
+  const rows = [];
+  const rowMap = {};
+  annotationTypes.forEach(type => {
+    rowMap[type] = mapAnnotationsToRows(
+      sequenceData[type],
+      sequenceLength,
+      bpsPerRow,
+      { splitForwardReverse: type === "primers" }
+    );
+  });
+
+  for (let rowNumber = 0; rowNumber < totalRows; rowNumber++) {
+    const row = {};
+    row.rowNumber = rowNumber;
+    row.start = rowNumber * bpsPerRow;
+    row.end =
+      (rowNumber + 1) * bpsPerRow - 1 < sequenceLength
+        ? (rowNumber + 1) * bpsPerRow - 1
+        : sequenceLength - 1;
+    if (row.end < 0) {
+      row.end = 0;
+    }
+    annotationTypes.forEach(type => {
+      row[type] = rowMap[type][rowNumber] || [];
+    });
+    row.sequence = sequenceData.sequence.slice(row.start, row.end + 1);
+
+    rows[rowNumber] = row;
+  }
+  return rows;
+};

package/src/prepareRowData.test.js

@@ -0,0 +1,36 @@
+
+
+import {expect} from "chai";
+
+import prepareRowData from "./prepareRowData";
+import output1 from "./prepareRowData_output1.json";
+
+describe("prepareRowData", () => {
+  it("maps overlapping annotations to rows correctly", () => {
+    const annotation1 = {
+      start: 0,
+      end: 9,
+      id: "a"
+    };
+    const annotation2 = {
+      start: 10,
+      end: 4,
+      id: "b"
+    };
+    const bpsPerRow = 5;
+    const sequenceData = {
+      sequence: "gagagagagagagaga",
+      features: [annotation1],
+      translations: [annotation1],
+      parts: { a: annotation1 },
+      cutsites: { b: annotation2 },
+      orfs: [annotation2],
+      primers: [annotation2, { id: "asdfa", start: 1, end: 3, forward: true }], //reverse primers shouldn't offset forward primers
+      warnings: [annotation2],
+      assemblyPieces: [annotation2],
+      lineageAnnotations: [annotation2]
+    };
+    const rowData = prepareRowData(sequenceData, bpsPerRow);
+    expect(rowData).to.deep.equal(output1);
+  });
+});

package/src/prepareRowData_output1.json

@@ -0,0 +1,391 @@
+[
+    {
+        "rowNumber": 0,
+        "start": 0,
+        "end": 4,
+        "features": [
+            {
+                "id": "a",
+                "annotation": {
+                    "start": 0,
+                    "end": 9,
+                    "id": "a"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "beginningAndEnd"
+            }
+        ],
+        "warnings": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "end"
+            }
+        ],
+        "assemblyPieces": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "end"
+            }
+        ],
+        "lineageAnnotations": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "end"
+            }
+        ],
+        "parts": [
+            {
+                "id": "a",
+                "annotation": {
+                    "start": 0,
+                    "end": 9,
+                    "id": "a"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "beginningAndEnd"
+            }
+        ],
+        "cutsites": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "end"
+            }
+        ],
+        "orfs": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "end"
+            }
+        ],
+        "translations": [
+            {
+                "id": "a",
+                "annotation": {
+                    "start": 0,
+                    "end": 9,
+                    "id": "a"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "beginningAndEnd"
+            }
+        ],
+        "primers": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 0,
+                "end": 4,
+                "yOffset": 0,
+                "enclosingRangeType": "end"
+            },
+            {
+                "id": "asdfa",
+                "annotation": {
+                    "id": "asdfa",
+                    "start": 1,
+                    "end": 3,
+                    "forward": true
+                },
+                "start": 1,
+                "end": 3,
+                "yOffset": 0,
+                "enclosingRangeType": "beginningAndEnd"
+            }
+        ],
+        "guides": [],
+        "sequence": "gagag"
+    },
+    {
+        "rowNumber": 1,
+        "start": 5,
+        "end": 9,
+        "features": [
+            {
+                "id": "a",
+                "annotation": {
+                    "start": 0,
+                    "end": 9,
+                    "id": "a"
+                },
+                "start": 5,
+                "end": 9,
+                "yOffset": 0,
+                "enclosingRangeType": "beginningAndEnd"
+            }
+        ],
+        "warnings": [],
+        "assemblyPieces": [],
+        "lineageAnnotations": [],
+        "parts": [
+            {
+                "id": "a",
+                "annotation": {
+                    "start": 0,
+                    "end": 9,
+                    "id": "a"
+                },
+                "start": 5,
+                "end": 9,
+                "yOffset": 0,
+                "enclosingRangeType": "beginningAndEnd"
+            }
+        ],
+        "cutsites": [],
+        "orfs": [],
+        "translations": [
+            {
+                "id": "a",
+                "annotation": {
+                    "start": 0,
+                    "end": 9,
+                    "id": "a"
+                },
+                "start": 5,
+                "end": 9,
+                "yOffset": 0,
+                "enclosingRangeType": "beginningAndEnd"
+            }
+        ],
+        "primers": [],
+        "guides": [],
+        "sequence": "agaga"
+    },
+    {
+        "rowNumber": 2,
+        "start": 10,
+        "end": 14,
+        "features": [],
+        "warnings": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 10,
+                "end": 14,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "assemblyPieces": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 10,
+                "end": 14,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "lineageAnnotations": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 10,
+                "end": 14,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "parts": [],
+        "cutsites": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 10,
+                "end": 14,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "orfs": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 10,
+                "end": 14,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "translations": [],
+        "primers": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 10,
+                "end": 14,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "guides": [],
+        "sequence": "gagag"
+    },
+    {
+        "rowNumber": 3,
+        "start": 15,
+        "end": 15,
+        "features": [],
+        "warnings": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 15,
+                "end": 15,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "assemblyPieces": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 15,
+                "end": 15,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "lineageAnnotations": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 15,
+                "end": 15,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "parts": [],
+        "cutsites": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 15,
+                "end": 15,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "orfs": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 15,
+                "end": 15,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "translations": [],
+        "primers": [
+            {
+                "id": "b",
+                "annotation": {
+                    "start": 10,
+                    "end": 4,
+                    "id": "b"
+                },
+                "start": 15,
+                "end": 15,
+                "yOffset": 0,
+                "enclosingRangeType": "beginning"
+            }
+        ],
+        "guides": [],
+        "sequence": "a"
+    }
+]