@teselagen/sequence-utils 0.1.22 → 0.1.23

package/src/cutSequenceByRestrictionEnzyme.test.js

@@ -0,0 +1,296 @@
+/* eslint-disable no-unused-expressions */
+
+
+import chai from "chai";
+import cutSequenceByRestrictionEnzyme from "./cutSequenceByRestrictionEnzyme.js";
+import enzymeList from "./aliasedEnzymesByName";
+
+const should = chai.should();
+describe("a simple, palindromic enzyme", () => {
+  //bamhi
+  // "bamhi": {
+  //     "name": "bamhi",
+  //     "site": "ggatcdc",
+  //     "forwardRegex": "g{2}atc{2}",
+  //     "reverseRegex": "g{2}atc{2}",
+  //     "topSnipOffset": 1,
+  //     "bottomSnipOffset": 5
+  // },
+  // ATGATCAGA
+  // 012345678
+  it.skip("cuts on the reverse strand and the recognition site wraps the origin", () => {
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "gcatccagagagagagagagagagagagagaaga",
+      true,
+      enzymeList["sapi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(0);
+    cutsites[0].end.should.equal(5);
+    cutsites[0].recognitionSiteRange.start.should.equal(0);
+    cutsites[0].recognitionSiteRange.end.should.equal(5);
+    cutsites[0].topSnipPosition.should.equal(1);
+    cutsites[0].bottomSnipPosition.should.equal(5);
+    cutsites[0].topSnipBeforeBottom.should.equal(true);
+    should.not.exist(cutsites[0].upstreamTopSnip);
+    should.not.exist(cutsites[0].upstreamBottomSnip);
+  });
+  it("cuts a single non-circular cutsite", () => {
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "GGATCC",
+      true,
+      enzymeList["bamhi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(0);
+    cutsites[0].end.should.equal(5);
+    cutsites[0].recognitionSiteRange.start.should.equal(0);
+    cutsites[0].recognitionSiteRange.end.should.equal(5);
+    cutsites[0].topSnipPosition.should.equal(1);
+    cutsites[0].bottomSnipPosition.should.equal(5);
+    cutsites[0].topSnipBeforeBottom.should.equal(true);
+    should.not.exist(cutsites[0].upstreamTopSnip);
+    should.not.exist(cutsites[0].upstreamBottomSnip);
+  });
+  it("cuts a single circular cutsite", () => {
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "CCrrrrGGAT",
+      true,
+      enzymeList["bamhi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(6);
+    cutsites[0].end.should.equal(1);
+    cutsites[0].recognitionSiteRange.start.should.equal(6);
+    cutsites[0].recognitionSiteRange.end.should.equal(1);
+    cutsites[0].topSnipPosition.should.equal(7);
+    cutsites[0].bottomSnipPosition.should.equal(1);
+    should.not.exist(cutsites[0].upstreamTopSnip);
+    should.not.exist(cutsites[0].upstreamBottomSnip);
+  });
+  it("does not cut a circular cutsite if sequence is non-circular", () => {
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "ccrrrrggat",
+      false,
+      enzymeList["bamhi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(0);
+  });
+  it("cuts multiple times", () => {
+    //bamhi
+    // "bamhi": {
+    //     "name": "bamhi",
+    //     "site": "ggatcdc",
+    //     "forwardRegex": "g{2}atc{2}",
+    //     "reverseRegex": "g{2}atc{2}",
+    //     "topSnipOffset": 1,
+    //     "bottomSnipOffset": 5
+    // },
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "ggatccttttggatcc",
+      true,
+      enzymeList["bamhi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(2);
+    cutsites[0].start.should.equal(0);
+    cutsites[0].end.should.equal(5);
+    cutsites[0].recognitionSiteRange.start.should.equal(0);
+    cutsites[0].recognitionSiteRange.end.should.equal(5);
+    cutsites[0].topSnipPosition.should.equal(1);
+    cutsites[0].bottomSnipPosition.should.equal(5);
+    should.not.exist(cutsites[0].upstreamTopSnip);
+    should.not.exist(cutsites[0].upstreamBottomSnip);
+    cutsites[1].start.should.equal(10);
+    cutsites[1].end.should.equal(15);
+    cutsites[1].recognitionSiteRange.start.should.equal(10);
+    cutsites[1].recognitionSiteRange.end.should.equal(15);
+    cutsites[1].topSnipPosition.should.equal(11);
+    cutsites[1].bottomSnipPosition.should.equal(15);
+    should.not.exist(cutsites[1].upstreamTopSnip);
+    should.not.exist(cutsites[1].upstreamBottomSnip);
+  });
+  it("it does not get into an infinite loop if the enzyme's forward/reverse regex are empty strings", () => {
+    // ttttttttttttttttttttrccggyttttttttttttttttttttt
+    // 01234567890123456789012345678901234567890123456
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "rccggyttttttttttttttttttttt",
+      false,
+      {
+        name: "fake enzyme",
+        site: "ccgcgg",
+        forwardRegex: "",
+        reverseRegex: "",
+        topSnipOffset: 1,
+        bottomSnipOffset: 1
+      }
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(0);
+    cutsites.error.should.not.be.null;
+    cutsites.error.should.equal(
+      "Cannot cut sequence. Enzyme restriction site must be at least 1 bp long."
+    );
+  });
+});
+describe("non-palindromic enzyme", () => {
+  // "bsmbi": {
+  //     "name": "BsmBI",
+  //     "site": "cgtctc",
+  //     "forwardRegex": "cgtctc",
+  //     "reverseRegex": "gagacg",
+  //     "topSnipOffset": 7,
+  //     "bottomSnipOffset": 11
+  // },
+  //
+  it("does not cut if the enzyme cuts outside of a linear sequence", () => {
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "cgtctc",
+      false,
+      enzymeList["bsmbi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(0);
+  });
+  it("does cut if the enzyme fits within circular sequence", () => {
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "cgtctc",
+      true,
+      enzymeList["bsmbi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(0);
+    cutsites[0].end.should.equal(4);
+    cutsites[0].recognitionSiteRange.start.should.equal(0);
+    cutsites[0].recognitionSiteRange.end.should.equal(5);
+    cutsites[0].topSnipPosition.should.equal(1);
+    cutsites[0].bottomSnipPosition.should.equal(5);
+    should.not.exist(cutsites[0].upstreamTopSnip);
+  });
+  it("does cut if the sequence is long enough", () => {
+    // 0123456 7890 12345678
+    // cgtctct tttt tttttttttttttttttt
+    // rrrrrr
+    //        |  dsTopSnip
+    //             |  dsBottomSnip
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "cgtctcttttttttttttttttttttttt",
+      true,
+      enzymeList["bsmbi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(0);
+    cutsites[0].end.should.equal(10);
+    cutsites[0].recognitionSiteRange.start.should.equal(0);
+    cutsites[0].recognitionSiteRange.end.should.equal(5);
+    cutsites[0].topSnipPosition.should.equal(7);
+    cutsites[0].bottomSnipPosition.should.equal(11);
+    should.not.exist(cutsites[0].upstreamTopSnip);
+    should.not.exist(cutsites[0].upstreamBottomSnip);
+  });
+  it("cuts on reverse strand", () => {
+    // 0123456 7890 12345678
+    // cgtctct tttt tttttttttttttttttt
+    // rrrrrr
+    //        |  dsTopSnip
+    //             |  dsBottomSnip
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "aaaaaaaaaaaaaaaaaaaaaaagagacg",
+      true,
+      enzymeList["bsmbi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(18);
+    cutsites[0].end.should.equal(28);
+    cutsites[0].recognitionSiteRange.start.should.equal(23);
+    cutsites[0].recognitionSiteRange.end.should.equal(28);
+    cutsites[0].topSnipPosition.should.equal(18);
+    cutsites[0].bottomSnipPosition.should.equal(22);
+    should.not.exist(cutsites[0].upstreamTopSnip);
+    should.not.exist(cutsites[0].upstreamBottomSnip);
+  });
+});
+describe("palindromic enzyme that cuts both upstream and downstream", () => {
+  // "nmedi": {
+  //     "name": "NmeDI",
+  //     "site": "rccggy",
+  //     "forwardRegex": "[agr]c{2}g{2}[cty]",
+  //     "reverseRegex": "[agr]c{2}g{2}[cty]",
+  //     "cutsTwice": true,
+  //     "topSnipOffset": 13,
+  //     "bottomSnipOffset": 18
+  // },
+  it("does not cut if the enzyme cuts outside of a linear sequence", () => {
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "rccggy",
+      false,
+      enzymeList["nmedi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(0);
+  });
+  it("does cut twice if the enzyme fits within linear sequence", () => {
+    // ttttttttttttttttttttrccggyttttttttttttttttttttt
+    // 01234567890123456789012345678901234567890123456
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "ttttttttttttttttttttrccggyttttttttttttttttttttt",
+      false,
+      enzymeList["nmedi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(8);
+    cutsites[0].end.should.equal(37);
+    cutsites[0].recognitionSiteRange.start.should.equal(20);
+    cutsites[0].recognitionSiteRange.end.should.equal(25);
+    cutsites[0].topSnipPosition.should.equal(33);
+    cutsites[0].bottomSnipPosition.should.equal(38);
+    cutsites[0].upstreamTopSnip.should.equal(12);
+    cutsites[0].upstreamBottomSnip.should.equal(7);
+  });
+  it("cuts only once if only the upstream cutting end fits within linear sequence", () => {
+    // ttttttttttttttttttttrccggyttttttttttttttttttttt
+    // 01234567890123456789012345678901234567890123456
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "ttttttttttttttttttttrccggy",
+      false,
+      enzymeList["nmedi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(8);
+    cutsites[0].end.should.equal(25);
+    cutsites[0].recognitionSiteRange.start.should.equal(20);
+    cutsites[0].recognitionSiteRange.end.should.equal(25);
+    should.not.exist(cutsites[0].topSnipPosition);
+    should.not.exist(cutsites[0].bottomSnipPosition);
+    cutsites[0].upstreamTopSnip.should.equal(12);
+    cutsites[0].upstreamBottomSnip.should.equal(7);
+  });
+  it("cuts only once if only the downstream cutting end fits within linear sequence", () => {
+    // ttttttttttttttttttttrccggyttttttttttttttttttttt
+    // 01234567890123456789012345678901234567890123456
+    const cutsites = cutSequenceByRestrictionEnzyme(
+      "rccggyttttttttttttttttttttt",
+      false,
+      enzymeList["nmedi"]
+    );
+    cutsites.should.be.an("array");
+    cutsites.length.should.equal(1);
+    cutsites[0].start.should.equal(0);
+    cutsites[0].end.should.equal(17);
+    cutsites[0].recognitionSiteRange.start.should.equal(0);
+    cutsites[0].recognitionSiteRange.end.should.equal(5);
+    cutsites[0].topSnipPosition.should.equal(13);
+    cutsites[0].bottomSnipPosition.should.equal(18);
+    should.not.exist(cutsites[0].upstreamTopSnip);
+    should.not.exist(cutsites[0].upstreamBottomSnip);
+  });
+});

package/src/defaultEnzymesByName.js

@@ -0,0 +1,278 @@
+import aliasedEnzymesByName from "./aliasedEnzymesByName";
+
+const defaultEnzymes = [
+  "aari",
+  "aatii",
+  "aaui",
+  "accebi",
+  "acci",
+  "accii",
+  "acciii",
+  "acsi",
+  "afai",
+  "aflii",
+  "alui",
+  "aor13hi",
+  "aor51hi",
+  "apai",
+  "apali",
+  "asci",
+  "asisi",
+  "asp35hi",
+  "asp713i",
+  "aspmi",
+  "atsi",
+  "atu1i",
+  "atu1ii",
+  "avrbi",
+  "avrii",
+  "bali",
+  "bamhi",
+  "banii",
+  "bari",
+  "baui",
+  "bbvbi",
+  "bcni",
+  "bcoki",
+  "bdii",
+  "bgli",
+  "bglii",
+  "blni",
+  "bme216i",
+  "bmet110i",
+  "bmgt120i",
+  "bmui",
+  "bnai",
+  "bpu1102i",
+  "bpuai",
+  "bpub5i",
+  "bsai",
+  "bsavi",
+  "bseri",
+  "bsgi",
+  "bshhi",
+  "bsiwi",
+  "bsmbi",
+  "bsmfi",
+  "bsofi",
+  "bsp105i",
+  "bsp1286i",
+  "bsp139i",
+  "bsp1407i",
+  "bsp4009i",
+  "bsp70i",
+  "bsp71i",
+  "bspa2i",
+  "bspci",
+  "bspfni",
+  "bspt104i",
+  "bspt107i",
+  "bsrfi",
+  "bsshii",
+  "bst1107i",
+  "bstb7si",
+  "bsthi",
+  "bstiz316i",
+  "bstli",
+  "bstpi",
+  "bstri",
+  "bstxi",
+  "bsu1532i",
+  "bsu8565i",
+  "bsu90i",
+  "btgai",
+  "btsci",
+  "btsi",
+  "bvei",
+  "ccini",
+  "ccop95i",
+  "ceqi",
+  "cfr10i",
+  "cfr45i",
+  "cfr47i",
+  "cfr6i",
+  "cjuii",
+  "clai",
+  "cpaai",
+  "cpoi",
+  "cspai",
+  "cspci",
+  "ddei",
+  "dpni",
+  "drai",
+  "dsai",
+  "dsavi",
+  "eaei",
+  "eagi",
+  "eam1105i",
+  "ecidi",
+  "ecl37i",
+  "eco211i",
+  "eco240i",
+  "eco241i",
+  "eco246i",
+  "eco247i",
+  "eco52i",
+  "eco68i",
+  "eco81i",
+  "eco93i",
+  "ecoicri",
+  "ecoo109i",
+  "ecoo65i",
+  "ecopi",
+  "ecoprri",
+  "ecori",
+  "ecorv",
+  "ecot14i",
+  "ecot22i",
+  "ecoviii",
+  "ehei",
+  "esphk22i",
+  "fbai",
+  "fdiii",
+  "foki",
+  "fsei",
+  "haeii",
+  "haeiii",
+  "hapii",
+  "hgiai",
+  "hgibi",
+  "hhai",
+  "hin1i",
+  "hincii",
+  "hindiii",
+  "hinfi",
+  "hpai",
+  "hpyf13iii",
+  "hpyf19ii",
+  "hpyf21i",
+  "hpyf28i",
+  "hpyf29i",
+  "hpyf36i",
+  "hpyf62i",
+  "hpyf65i",
+  "hpyii",
+  "koyi",
+  "kpni",
+  "m.bbu297i",
+  "m.pmudam",
+  "maek81i",
+  "mboi",
+  "mboii",
+  "mfli",
+  "mizi",
+  "mlui",
+  "mph1103ii",
+  "msei",
+  "msii",
+  "mspi",
+  "mthai",
+  "muni",
+  "naei",
+  "ncoi",
+  "ndai",
+  "ndei",
+  "nflaii",
+  "ngbi",
+  "ngobviii",
+  "ngodviii",
+  "ngoeii",
+  "ngotii",
+  "nhei",
+  "nlaiv",
+  "noci",
+  "noti",
+  "novii",
+  "nrui",
+  "nsbi",
+  "nsici",
+  "nsp29132i",
+  "paci",
+  "pae17ki",
+  "pca17ai",
+  "pfaaiii",
+  "pfl16i",
+  "ple214i",
+  "pmaci",
+  "pmei",
+  "pru2i",
+  "psb9879i",
+  "pshai",
+  "pshbi",
+  "psp1406i",
+  "psp31i",
+  "psp33i",
+  "psp5i",
+  "psti",
+  "psuni",
+  "pvui",
+  "pvuii",
+  "ral8i",
+  "rsplki",
+  "saci",
+  "sacii",
+  "sali",
+  "sapi",
+  "sau3ai",
+  "sauni",
+  "sbai",
+  "sbfi",
+  "scai",
+  "sfii",
+  "sflhk115731i",
+  "slu1777i",
+  "smai",
+  "smii",
+  "snabi",
+  "spei",
+  "sphi",
+  "srfi",
+  "srl61di",
+  "sse8387i",
+  "ssp2i",
+  "sspi",
+  "stui",
+  "suii",
+  "swai",
+  "taqi",
+  "tauii",
+  "tsci",
+  "tth111i",
+  "tthhb8i",
+  "uba1093i",
+  "uba1095i",
+  "uba1122i",
+  "uba1160i",
+  "uba1229i",
+  "uba1371i",
+  "uba1380i",
+  "uba1403i",
+  "uba1415i",
+  "uba1437i",
+  "uba1439i",
+  "uba1440i",
+  "uba36i",
+  "uba41i",
+  "uba42i",
+  "uba89i",
+  "uban13i",
+  "van91i",
+  "vcho66i",
+  "vpak11bi",
+  "vpakutji",
+  "xbai",
+  "xcyi",
+  "xhoi",
+  "xmai",
+  "xmli",
+  "xphi",
+  "xspi"
+];
+
+const defaultEnzymesByName = {};
+
+defaultEnzymes.forEach(name => {
+  defaultEnzymesByName[name] = aliasedEnzymesByName[name];
+});
+
+export default defaultEnzymesByName;

package/src/degenerateDnaToAminoAcidMap.js

@@ -0,0 +1,5 @@
+import {invert} from "lodash";
+import aminoAcidToDegenerateDnaMap from "./aminoAcidToDegenerateDnaMap";
+
+const degenerateDnaToAminoAcidMap = invert(aminoAcidToDegenerateDnaMap);
+export default degenerateDnaToAminoAcidMap;

package/src/degenerateRnaToAminoAcidMap.js

@@ -0,0 +1,5 @@
+import {invert} from "lodash";
+import aminoAcidToDegenerateRnaMap from "./aminoAcidToDegenerateRnaMap";
+
+const degenerateRnaToAminoAcidMap = invert(aminoAcidToDegenerateRnaMap);
+export default degenerateRnaToAminoAcidMap;

package/src/deleteSequenceDataAtRange.js

@@ -0,0 +1,5 @@
+import insertSequenceDataAtPositionOrRange from "./insertSequenceDataAtPositionOrRange";
+
+export default function deleteSequenceDataAtRange(sequenceData, range) {
+  return insertSequenceDataAtPositionOrRange({}, sequenceData, range);
+};