@datagrok/bio 2.4.11 → 2.4.12

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.4.11",
+  "version": "2.4.12",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.28.0",
+    "@datagrok-libraries/bio": "^5.28.4",
     "@datagrok-libraries/chem-meta": "^1.0.1",
     "@datagrok-libraries/ml": "^6.3.16",
     "@datagrok-libraries/utils": "^2.1.3",

package/src/package-test.ts

@@ -21,6 +21,7 @@ import './tests/similarity-diversity-tests';
 import './tests/substructure-filters-tests';
 import './tests/pepsea-tests';
 import './tests/viewers';
+import './tests/units-handler-tests';
 
 // Tests hanging github CI
 import './tests/activity-cliffs-tests';

package/src/tests/units-handler-tests.ts

@@ -0,0 +1,97 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {ALPHABET, NOTATION, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+
+const seqDna = `seq
+ACGTC
+CAGTGT
+TTCAAC
+`;
+
+const seqDnaMsa = `seq
+AC-GT-CT
+CAC-T-GT
+ACCGTACT
+`;
+
+const seqUn = `seq
+abc-dfgg-abc1-cfr3-rty-wert
+rut12-her2-rty-wert-abc-abc1-dfgg
+rut12-rty-her2-abc-cfr3-wert-rut12
+`;
+
+const seqHelm = `seq
+PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$
+PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV.Phe_ab-dehydro.N.D-Orn.D-aThr.Phe_4Me}$$$$
+PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV.Thr_PO3H2.N.D-Orn.D-aThr.Phe_4Me}$$$$
+PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV.Thr_PO3H2.N.D-Orn.D-aThr.Phe_4Me}$$$$
+`;
+
+category('UnitsHandler', () =>{
+  test('Seq-Fasta', async () =>{
+    const [df, uh] = await loadCsvWithDetection(seqDna);
+    expect(uh.notation, NOTATION.FASTA);
+    expect(uh.isMsa(), false);
+  });
+
+  test('Seq-Fasta-MSA', async () =>{
+    const [df, uh] = await loadCsvWithDetection(seqDnaMsa);
+    expect(uh.notation, NOTATION.FASTA);
+    expect(uh.isMsa(), true);
+  });
+
+  test('Seq-Fasta-units', async () =>{
+    const [df, uh] = await loadCsvWithTag(seqDna, DG.TAGS.UNITS, NOTATION.FASTA);
+    expect(uh.notation, NOTATION.FASTA);
+    expect(uh.isMsa(), false);
+  });
+
+  test('Seq-Fasta-MSA-units', async () =>{
+    const [df, uh] = await loadCsvWithTag(seqDnaMsa, DG.TAGS.UNITS, NOTATION.FASTA);
+    expect(uh.notation, NOTATION.FASTA);
+    expect(uh.isMsa(), true);
+  });
+
+  test('Seq-Helm', async () =>{
+    const [df, uh] = await loadCsvWithTag(seqHelm, DG.TAGS.UNITS, NOTATION.HELM);
+    expect(uh.notation, NOTATION.HELM);
+    expect(uh.isHelm(), true);
+  });
+
+  test('Seq-UN', async () =>{
+    const [df, uh] = await loadCsvWithTag(seqUn, DG.TAGS.UNITS, NOTATION.SEPARATOR);
+    expect(uh.notation, NOTATION.SEPARATOR);
+    expect(uh.separator, '-');
+    expect(uh.alphabet, ALPHABET.UN);
+  });
+
+  test('Seq-UN-auto', async () =>{
+    const [df, uh] = await loadCsvWithDetection(seqUn);
+    expect(uh.notation, NOTATION.SEPARATOR);
+    expect(uh.separator, '-');
+    expect(uh.alphabet, ALPHABET.UN);
+  });
+
+  async function loadCsvWithDetection(csv: string): Promise<[df: DG.DataFrame, uh: UnitsHandler]> {
+    const df = DG.DataFrame.fromCsv(csv);
+    await grok.data.detectSemanticTypes(df);
+    const uh = new UnitsHandler(df.getCol('seq'));
+    return [df, uh];
+  }
+
+  async function loadCsvWithTag(csv: string, tag: string, value: string):
+    Promise<[df: DG.DataFrame, uh: UnitsHandler]> {
+    const df = DG.DataFrame.fromCsv(csv);
+    const col = df.getCol('seq');
+    col.setTag(tag, value);
+    col.semType = DG.SEMTYPE.MACROMOLECULE;
+    if (value === NOTATION.SEPARATOR)
+      col.setTag(TAGS.separator, '-');
+    const uh = new UnitsHandler(df.getCol('seq'));
+    return [df, uh];
+  }
+});