adding aliasedEnzymesByName and defaultEnzymesByName; removing old en…

…zymeList
TeselaGen · Oct 9, 2020 · a9fa562 · a9fa562
1 parent 3e4d343
commit a9fa562
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Showing 11 changed files with 15,056 additions and 7,316 deletions.
diff --git a/scratch/enzymeList.js b/scratch/enzymeList.js
diff --git a/scratch/test.js b/scratch/test.js
@@ -0,0 +1,151 @@
+const { uniq, filter } = require("lodash");
+const aliasedEnzymes = require("./aliasedEnzymes.json");
+const enzymesKeyedByName = {};
+aliasedEnzymes.forEach((enz) => {
+  enz.name.forEach((name) => {
+    enzymesKeyedByName[name.toLowerCase()] = enz;
+  });
+});
+
+const defaultEnzymes = [
+  "aatii",
+  "acci",
+  "accii",
+  "acciii",
+  "afai",
+  "aflii",
+  "alui",
+  "aor13hi",
+  "aor51hi",
+  "apai",
+  "apali",
+  "asci",
+  "asisi",
+  "avrii",
+  "bali",
+  "bamhi",
+  "banii",
+  "bcni",
+  "bgli",
+  "bglii",
+  "blni",
+  "bmet110i",
+  "bmgt120i",
+  "bpu1102i",
+  "bsai",
+  "bsgi",
+  "bsmbi",
+  "bsp1286i",
+  "bsp1407i",
+  "bspt104i",
+  "bspt107i",
+  "bsshii",
+  "bst1107i",
+  "bstpi",
+  "bstxi",
+  "cfr10i",
+  "clai",
+  "cpoi",
+  "ddei",
+  "dpni",
+  "drai",
+  "eaei",
+  "eagi",
+  "eam1105i",
+  "eco52i",
+  "eco81i",
+  "ecoo109i",
+  "ecoo65i",
+  "ecori",
+  "ecorv",
+  "ecot14i",
+  "ecot22i",
+  "fbai",
+  "foki",
+  "fsei",
+  "haeii",
+  "haeiii",
+  "hapii",
+  "hhai",
+  "hin1i",
+  "hincii",
+  "hindiii",
+  "hinfi",
+  "hpai",
+  "kpni",
+  "mboi",
+  "mboii",
+  "mfli",
+  "mlui",
+  "msei",
+  "mspi",
+  "muni",
+  "naei",
+  "ncoi",
+  "ndei",
+  "nhei",
+  "noti",
+  "nrui",
+  "nsbi",
+  "paci",
+  "pmaci",
+  "pmei",
+  "pshai",
+  "pshbi",
+  "psp1406i",
+  "psti",
+  "pvui",
+  "pvuii",
+  "saci",
+  "sacii",
+  "sali",
+  "sapi",
+  "sau3ai",
+  "sbfi",
+  "scai",
+  "sfii",
+  "smai",
+  "smii",
+  "snabi",
+  "spei",
+  "sphi",
+  "srfi",
+  "sse8387i",
+  "sspi",
+  "stui",
+  "swai",
+  "taqi",
+  "tth111i",
+  "van91i",
+  "vpak11bi",
+  "xbai",
+  "xhoi",
+  "xmai",
+  "xspi",
+];
+
+const defaultEnzymesByHash = {}
+const defaultEnzymesFull = [];
+defaultEnzymes.forEach((name, index) => {
+  const fullEnz = enzymesKeyedByName[name]
+  fullEnz["canonicalName" + index] = name
+  const hash = getEnzymeHash(fullEnz)
+  const existing =  defaultEnzymesByHash[hash]  || []
+  defaultEnzymesByHash[hash] = [fullEnz].concat(existing);
+
+  defaultEnzymesFull.push(fullEnz);
+});
+
+// console.log(`defaultEnzymesFull.length:`, defaultEnzymesFull.length);
+// console.log(
+//   `uniq(defaultEnzymesFull).length:`,
+//   uniq(defaultEnzymesFull).length
+// );
+const dups = filter(defaultEnzymesByHash, (z) => z.length > 1)
+console.log(`dups.length:`,dups.length)
+console.log(`dups:`,dups)
+
+
+function getEnzymeHash(z) {
+  return `${z.site}-${z.topSnipOffset}-${z.bottomSnipOffset}-${z.cutType}-${z.usForward}-${z.usReverse}`;
+}