@teselagen/sequence-utils 0.3.38-beta.3 → 0.3.42

package/src/computeDigestFragments.ts

@@ -1,238 +0,0 @@
-import shortid from "shortid";
-import { flatMap, cloneDeep } from "lodash-es";
-import {
-  normalizePositionByRangeLength,
-  getRangeLength
-} from "@teselagen/range-utils";
-import getCutsitesFromSequence from "./getCutsitesFromSequence";
-import { CutSite, DigestFragment, RestrictionEnzyme } from "./types";
-
-// Explicitly define the params interface
-export interface ComputeDigestFragmentsParams {
-  cutsites: CutSite[];
-  sequenceLength: number;
-  circular: boolean;
-  includeOverAndUnderHangs?: boolean;
-  computePartialDigest?: boolean;
-  computeDigestDisabled?: boolean;
-  computePartialDigestDisabled?: boolean;
-  selectionLayerUpdate?: (params: {
-    start: number;
-    end: number;
-    name: string;
-  }) => void;
-  updateSelectedFragment?: (id: string) => void;
-}
-
-export function computeDigestFragments({
-  cutsites,
-  sequenceLength,
-  circular,
-  //optional:
-  includeOverAndUnderHangs,
-  computePartialDigest,
-  computeDigestDisabled,
-  computePartialDigestDisabled,
-  selectionLayerUpdate,
-  updateSelectedFragment
-}: ComputeDigestFragmentsParams) {
-  const fragments: DigestFragment[] = [];
-  const overlappingEnzymes: DigestFragment[] = [];
-  const pairs: CutSite[][] = [];
-
-  const sortedCutsites = cutsites.filter(
-    (
-      c
-    ): c is CutSite & { topSnipPosition: number; bottomSnipPosition: number } =>
-      c.topSnipPosition != null && c.bottomSnipPosition != null
-  );
-  if (!circular && cutsites.length) {
-    sortedCutsites.push({
-      id: "seqTerm_" + shortid(),
-      start: 0,
-      end: 0,
-      overhangBps: "",
-      topSnipPosition: 0,
-      bottomSnipPosition: 0,
-      overhangSize: 0, // Added to satisfy CutSite
-      upstreamTopSnip: 0,
-      upstreamBottomSnip: 0,
-      upstreamTopBeforeBottom: false,
-      topSnipBeforeBottom: false,
-      recognitionSiteRange: {
-        start: 0,
-        end: 0
-      },
-      forward: true,
-      name: "Sequence_Terminus",
-      type: "START_OR_END_OF_SEQ",
-      restrictionEnzyme: {
-        name: "Sequence_Terminus",
-        site: "",
-        forwardRegex: "",
-        reverseRegex: ""
-      }
-    });
-  }
-
-  sortedCutsites.sort((a, b) => {
-    return a.topSnipPosition - b.topSnipPosition;
-  });
-
-  sortedCutsites.forEach((cutsite1, index) => {
-    if (!computeDigestDisabled) {
-      pairs.push([
-        cutsite1,
-        sortedCutsites[index + 1]
-          ? sortedCutsites[index + 1]
-          : sortedCutsites[0]
-      ]);
-    }
-    if (computePartialDigest && !computePartialDigestDisabled) {
-      sortedCutsites.forEach((cs, index2) => {
-        // Filter out adjacent cutsites (standard digest handles these)
-        const isAdjacent =
-          index2 === index + 1 ||
-          (index === sortedCutsites.length - 1 && index2 === 0);
-        if (isAdjacent) {
-          return;
-        }
-        pairs.push([cutsite1, sortedCutsites[index2]]);
-      });
-    }
-  });
-
-  pairs.forEach(r => {
-    let [cut1, cut2] = r;
-
-    let start: number;
-    let end: number;
-    let size: number;
-    start = normalizePositionByRangeLength(
-      cut1.topSnipPosition!,
-      sequenceLength
-    );
-    end = normalizePositionByRangeLength(
-      cut2.topSnipPosition! - 1,
-      sequenceLength
-    );
-    size = getRangeLength({ start, end }, sequenceLength);
-    let overlapsSelf: boolean | undefined;
-    if (includeOverAndUnderHangs) {
-      const oldSize = size;
-      start = normalizePositionByRangeLength(
-        cut1.topSnipBeforeBottom
-          ? cut1.topSnipPosition!
-          : cut1.bottomSnipPosition!,
-        sequenceLength
-      );
-      end = normalizePositionByRangeLength(
-        cut2.topSnipBeforeBottom
-          ? cut2.bottomSnipPosition! - 1
-          : cut2.topSnipPosition! - 1,
-        sequenceLength
-      );
-      size = getRangeLength({ start, end }, sequenceLength);
-      if (oldSize > size) {
-        //we've got a part that wraps on itself
-        overlapsSelf = true;
-        size += sequenceLength;
-      }
-    }
-
-    let isFormedFromLinearEnd: boolean | undefined;
-    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";
-    }
-
-    // Add isOverhangIncludedInFragmentSize logic
-    cut1 = {
-      ...cut1,
-      isOverhangIncludedInFragmentSize:
-        cut1.name !== "Linear_Sequence_Start" &&
-        cut1.name !== "Sequence_Terminus" &&
-        (cut1.overhangSize || 0) > 0 &&
-        !!cut1.topSnipBeforeBottom
-    };
-    cut2 = {
-      ...cut2,
-      isOverhangIncludedInFragmentSize:
-        cut2.name !== "Linear_Sequence_End" &&
-        cut2.name !== "Sequence_Terminus" &&
-        (cut2.overhangSize || 0) > 0 &&
-        !cut2.topSnipBeforeBottom
-    };
-
-    const id = start + "-" + end + "-" + size + "-";
-    const name = `${cut1.restrictionEnzyme.name} -- ${cut2.restrictionEnzyme.name} ${size} bps`;
-    // getRangeLength({ start, end }, sequenceLength);
-
-    fragments.push({
-      isFormedFromLinearEnd,
-      madeFromOneCutsite: cut1.id === cut2.id,
-      start,
-      end,
-      size,
-      overlapsSelf,
-      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
-  };
-}
-
-export function getDigestFragsForSeqAndEnzymes({
-  sequence,
-  circular,
-  enzymes,
-  includeOverAndUnderHangs
-}: {
-  sequence: string;
-  circular: boolean;
-  enzymes: RestrictionEnzyme[];
-  includeOverAndUnderHangs?: boolean;
-}) {
-  const cutsitesByName = getCutsitesFromSequence(sequence, circular, enzymes);
-  const digest = computeDigestFragments({
-    includeOverAndUnderHangs,
-    cutsites: flatMap(cutsitesByName) as CutSite[],
-    sequenceLength: sequence.length,
-    circular
-  });
-  digest.fragments.sort((a, b) => b.size - a.size);
-  return digest;
-}

package/src/condensePairwiseAlignmentDifferences.ts

@@ -1,85 +0,0 @@
-export default function condensePairwiseAlignmentDifferences(
-  referenceSeq: string,
-  alignedSeq: string
-): string {
-  const overviewMinimapTrack: string[] = [];
-  const referenceSeqSplit = referenceSeq.toLowerCase().split("");
-  const alignedSeqSplit = alignedSeq.toLowerCase().split("");
-  const seqLength = alignedSeq.length;
-  const alignedSeqWithoutLeadingDashes = alignedSeq.replace(/^-+/g, "");
-  const alignedSeqWithoutTrailingDashes = alignedSeq.replace(/-+$/g, "");
-
-  const startIndex = seqLength - alignedSeqWithoutLeadingDashes.length;
-  const endIndex =
-    seqLength - (seqLength - alignedSeqWithoutTrailingDashes.length);
-  for (let i = 0; i < referenceSeqSplit.length; i++) {
-    if (i < startIndex || i >= endIndex) {
-      overviewMinimapTrack.push("W");
-    } else if (
-      referenceSeqSplit[i] === alignedSeqSplit[i] &&
-      referenceSeqSplit[i] !== "-" &&
-      alignedSeqSplit[i] !== "-"
-    ) {
-      // ACTG match
-      overviewMinimapTrack.push("G");
-    } else if (
-      referenceSeqSplit[i] !== alignedSeqSplit[i] &&
-      referenceSeqSplit[i] !== "-" &&
-      alignedSeqSplit[i] !== "-"
-    ) {
-      // ACTG mismatch
-      overviewMinimapTrack.push("R");
-    } else if (alignedSeqSplit[i] === "-") {
-      // deletion
-      overviewMinimapTrack.push("R");
-    } else if (
-      referenceSeqSplit[i] === "-" &&
-      referenceSeqSplit[i - 1] !== "-" &&
-      i !== referenceSeqSplit.length - 1 &&
-      referenceSeqSplit[i + 1] === "-"
-    ) {
-      // insertion (first "-" of a >1 insertion)
-      overviewMinimapTrack.push("R");
-    } else if (
-      referenceSeqSplit[i] === "-" &&
-      referenceSeqSplit[i - 1] !== "-" &&
-      i !== referenceSeqSplit.length - 1 &&
-      referenceSeqSplit[i + 1] !== "-"
-    ) {
-      // "-" of a one-bp insertion in the middle of the sequence
-      overviewMinimapTrack.push("R");
-      i++;
-    } else if (
-      i === referenceSeqSplit.length - 1 &&
-      referenceSeqSplit[i] === "-" &&
-      referenceSeqSplit[i - 1] === "-"
-    ) {
-      // final "-" of a >1 insertion at the 3' end of the sequence
-      overviewMinimapTrack.splice(-2, 1);
-    } else if (
-      i === referenceSeqSplit.length - 1 &&
-      referenceSeqSplit[i] === "-" &&
-      referenceSeqSplit[i - 1] !== "-"
-    ) {
-      // "-" of a one-bp insertion at the 3' end of the sequence
-      overviewMinimapTrack.pop();
-      overviewMinimapTrack.push("R");
-    } else if (
-      referenceSeqSplit[i] === "-" &&
-      referenceSeqSplit[i - 1] === "-" &&
-      referenceSeqSplit[i + 1] !== "-"
-    ) {
-      // "-" at the end of an insertion
-      i++;
-    } else if (
-      referenceSeqSplit[i] === "-" &&
-      referenceSeqSplit[i - 1] === "-"
-    ) {
-      // insertion (NOT first "-" of the insertion)
-      // do nothing, skip over these "-"
-    } else {
-      console.error("should not reach this step!");
-    }
-  }
-  return overviewMinimapTrack.join("");
-}

package/src/convertAACaretPositionOrRangeToDna.ts

@@ -1,28 +0,0 @@
-import { Range } from "./types";
-
-export default function convertAACaretPositionOrRangeToDna(
-  rangeOrCaret: Range | number
-): Range | number {
-  if (typeof rangeOrCaret === "object" && rangeOrCaret !== null) {
-    return convertAARangeToDnaRange({
-      ...rangeOrCaret,
-      locations: rangeOrCaret.locations
-        ? rangeOrCaret.locations.map(convertAARangeToDnaRange)
-        : undefined
-    });
-  } else {
-    return convertAACaretPositionToDnaCaretPosition(rangeOrCaret as number);
-  }
-}
-
-function convertAACaretPositionToDnaCaretPosition(caret: number): number {
-  return caret * 3;
-}
-
-function convertAARangeToDnaRange(range: Range): Range {
-  return {
-    ...range,
-    start: range.start > -1 ? range.start * 3 : range.start,
-    end: range.end > -1 ? range.end * 3 + 2 : range.end
-  };
-}

package/src/convertDnaCaretPositionOrRangeToAA.ts

@@ -1,28 +0,0 @@
-import { Range } from "./types";
-
-export default function convertDnaCaretPositionOrRangeToAA(
-  rangeOrCaret: Range | number
-): Range | number {
-  if (typeof rangeOrCaret === "object" && rangeOrCaret !== null) {
-    return convertDnaRangeToAARange({
-      ...rangeOrCaret,
-      locations: rangeOrCaret.locations
-        ? rangeOrCaret.locations.map(convertDnaRangeToAARange)
-        : undefined
-    });
-  } else {
-    return convertDnaCaretPositionToAACaretPosition(rangeOrCaret as number);
-  }
-}
-
-function convertDnaCaretPositionToAACaretPosition(caret: number): number {
-  return Math.floor(caret / 3);
-}
-
-function convertDnaRangeToAARange(range: Range): Range {
-  return {
-    ...range,
-    start: range.start > -1 ? Math.floor(range.start / 3) : range.start,
-    end: range.end > -1 ? Math.floor(range.end - 2) / 3 : range.end
-  };
-}