@datagrok/bio 1.7.5 → 1.7.8

package/files/tests/testActivityCliffs.csv

@@ -0,0 +1,311 @@
+chembl_tid,smiles,Activity
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+CHEMBL260,O=C1C2=CC=C(NC3=CC=C(F)C=C3F)C=C2OCC2=C(OC[C@H](O)CO)C=CC=C12,7.37675
+CHEMBL260,O=C1C2=CC(OCCC3CCOCC3)=CC=C2COC2=CC(NC3=CC=C(F)C=C3F)=CC=C12,6.77064
+CHEMBL260,COC1=CC=CC2=C1COC1=CC(NC3=CC=C(F)C=C3F)=CC=C1C2=O,7.20066
+CHEMBL260,COC1=CC=CC2=C1COC1=CC(NC3=CC=CC=C3N)=CC=C1C2=O,7.02687
+CHEMBL260,O=C1C2=CC=C(NC3=CC=C(F)C=C3F)C=C2OCC2=C(OCCN3CCOCC3)C=CC=C12,7.46852
+CHEMBL5260,CNS(=O)(=O)C1=CC=CC(NC2=NC=NC3=C2C=C[NH]3)=C1,7.09691
+CHEMBL5260,CNS(=O)(=O)C1=CC=CC(OC2=NC=NC3=C2C=C[NH]3)=C1,4.79588
+CHEMBL5260,CNS(=O)(=O)C1=CC=CC(NC2=CC=NC(NC3=CC=CC(C)=C3)=C2)=C1,5.30103
+CHEMBL1075104,FC(F)(F)C1=CC=CC(SC2=NN3C(C4=CC=CS4)=NC=C3C=C2)=C1,5.05535
+CHEMBL1075104,N#CC1=CC=CC(C2=C[NH]C3=NC=NC(N4CCOCC4)=C23)=C1,7.97686
+CHEMBL1075104,N#CC1=CN=CC(C2=C[NH]C3=NC=NC(N4CCOCC4)=C23)=C1,5.41485
+CHEMBL1075104,O=C(NC1=CN=CC=N1)C1=CC(Br)=CC=C1OCC1=CC=CC=C1,5.70000
+CHEMBL1075104,O=C(NC1=CN=CC=N1)C1=CC(Br)=CC=C1OCC1=CC=CC=C1,5.70000
+CHEMBL5407,COC1=CC=C2C(=O)/C(=C/C3=C[NH]C4=NC=CC=C34)OC2=C1CN1CCNCC1,8.88606
+CHEMBL5407,N[C@H]1CCCN(C2=NC=NC=C2NC2=CC=CC3=CN=C(C4=C(F)C=CC=C4F)N=C23)C1,5.40894
+CHEMBL2185,CC1=CC(NC2=NC(SC3=CC=C(NC(=O)CN4C[C@H](SC(C)(C)C)C[C@H]4CO)C=C3)=NN3C=CC=C23)=N[NH]1,5.74715
+CHEMBL2185,CCOC(=O)C1=C2NC3=C(C(=O)CCC3)C(C3=CC=NC(SC4=NC5=CC=CC=C5[NH]4)=C3)C2=C[NH]1,5.95861
+CHEMBL2185,CCOC(=O)C1=C2NC3=C(C(=O)CCC3)C(C3=CC=NC(SC4=NC5=CC=CC=C5[NH]4)=C3)C2=C[NH]1,5.95861
+CHEMBL4896,O=C(NCC1CCCNC1)C1=CC=NC2=C1N=C(C1=CC=CS1)[NH]2,7.13077
+CHEMBL4896,O=C(N[C@H]1CCCNC1)C1=CC=NC2=C1[NH]C(C1=CC(N3CCOCC3)=CS1)=N2,4.65758
+CHEMBL4896,NC1CCCC(NC(=O)C2=CC=NC3=C2[NH]C(C2=CC=CS2)=N3)C1,7.45593
+CHEMBL5284,COC1=CC=CC=C1NC1=NC=CC(C2=CC=C(C(N)=O)C(C(C)C)=C2)=N1,5.80000
+CHEMBL4203,C1=CN=CC(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)=C1,7.20066
+CHEMBL4203,C1=CN=CC(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)=C1,7.20066
+CHEMBL4203,C1=CN=CC(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)=C1,7.20066
+CHEMBL4203,C1=CN=CC(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)=C1,7.20066
+CHEMBL4203,C1=CN=CC(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)=C1,7.74743
+CHEMBL4203,ClC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1Cl,7.62591
+CHEMBL4203,ClC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1Cl,7.62591
+CHEMBL4203,BrC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1Br,7.42082
+CHEMBL4203,C1=NC=C(CNC2=CC=NC(C3=CC=C4OCOC4=C3)=N2)C=N1,4.58503
+CHEMBL4203,ClC1=CC=C(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)C=C1,7.30103
+CHEMBL4203,BrC1=CC(Br)=CC(CNC2=NC=CC(C3=CC=C4OCOC4=C3)=N2)=C1,7.72185
+CHEMBL4203,COC1=CC=C(C2=NC=CC(NCC3=CC=C(Cl)C(Cl)=C3)=N2)C=C1,4.83565
+CHEMBL4204,CCN1CCN(CC2=CC=C(NC(=O)COC3=CC=C(C4=CC=NC=C4)C=C3)C=C2C(F)(F)F)CC1,5.71897
+CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3CCC3)=NC=C2C2=NC3=CC=CC=C3S2)[C@H](O)[C@@H]1O,3.39470
+CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3=CN=CN=C3)=NC=C2C2=NC3=CC=CC=C3S2)[C@H](O)[C@@H]1O,5.22185
+CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3=CN=CN=C3)=NC=C2C2=NC3=CC=CC=C3S2)[C@H](O)[C@@H]1O,5.22185
+CHEMBL3778,CN1C=C(NC(=O)C2=C3N=C(OCCN)C=CN3N=C2)C(C(N)=O)=N1,5.03621
+CHEMBL3778,CC1=CC(NC2=NC=C(C3=NC4=CN=CC=C4S3)C(N[C@@H]3C[C@H](CO)[C@@H](O)[C@H]3O)=N2)=CC=N1,8.52288
+CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3=CN=CN=C3)=NC=C2C2=NC3=CN=CC=C3S2)[C@H](O)[C@@H]1O,7.92082
+CHEMBL3778,OC[C@H]1C[C@@H](NC2=NC(NC3=CN=CN=C3)=NC=C2C2=NC3=CC=NC=C3S2)[C@H](O)[C@@H]1O,8.22185
+CHEMBL3886,O=S(=O)(NC1=CC=C(F)C(C#CC2=CN=C3[NH]N=CC3=C2)=C1F)C1=CC=CC(Cl)=C1,8.29243
+CHEMBL4523,O=C(O)C1=CC2=CC(Br)=CC(N[C@H]3CC[C@@H](O)CC3)=C2O1,5.16749
+CHEMBL4523,FC1=CC=CC(F)=C1C1=CC=C2[NH]N=C(C3=CN=CC(N4CCNCC4)=N3)C2=C1,7.53760
+CHEMBL4523,N[C@H]1CCCN(C2=NC=NC=C2NC2=NC=C3C=CC(C4=C(F)C=CC=C4F)=NN23)C1,6.95861
+CHEMBL4247,COC1=CC(C2CCN(CC(N)=O)CC2)=CC=C1NC1=NN2C(C3=NC=CC=C3OC)=CC=C2C=N1,5.97428
+CHEMBL4247,COC1=CC(C2CCN(CC(N)=O)CC2)=CC=C1NC1=NN2C(C3=NC=CC=C3OC)=CC=C2C=N1,5.97428
+CHEMBL4247,CC1=CC(NC2=NC=C(Cl)C(NC3=CC=CC=C3S(=O)(=O)C(C)C)=N2)=C(OC(C)C)C=C1C1CCN(C)CC1,7.93930
+CHEMBL4247,CC1=CC(NC2=NC=C(Cl)C(NC3=CN(C)N=C3S(=O)(=O)N(C)C)=N2)=C(OC(C)C)C=C1C1CCNCC1,5.17503
+CHEMBL4816,CNC1=NC=CC(C2=CC=C(C(=O)N[C@H](CO)CC3=CC=C(Cl)C=C3Cl)S2)=N1,6.55284

package/files/tests/testCereal.csv

@@ -0,0 +1,78 @@
+cereal_name,Calories,Carbohydrates,Fat,Fiber,Potassium,Protein,Sodium,Sugar,Vitamins/Minerals
+Mueslix_Crispy_Blend,160,17,2,3,160,3,150,13,25
+"Muesli_Raisins,_Dates,_&_Almonds",150,16,3,3,170,4,95,11,25
+"Muesli_Raisins,_Peaches,_&_Pecans",150,16,3,3,170,4,150,11,25
+Just_Right_Fruit_&_Nut,140,20,1,2,95,3,170,9,100
+Nutri-Grain_Almond-Raisin,140,21,2,3,130,3,220,7,25
+Total_Raisin_Bran,140,15,1,4,230,3,190,14,100
+Basic_4,130,18,2,2,100,3,210,8,25
+Oatmeal_Raisin_Crisp,130,null,2,null,120,3,170,10,25
+100%_Natural_Bran,120,8,5,2,135,3,15,8,0
+Cap'n'Crunch,120,12,2,0,35,1,220,12,25
+Cinnamon_Toast_Crunch,120,13,3,0,45,1,210,9,25
+"Fruit_&_Fibre_Dates,_Walnuts,_and_Oats",120,12,2,5,200,3,160,10,25
+Fruitful_Bran,120,14,0,5,190,3,240,12,25
+Great_Grains_Pecan,120,13,3,3,100,3,75,4,25
+Honey_Graham_Ohs,120,12,2,1,45,1,220,11,25
+Nut&Honey_Crunch,120,15,1,0,40,2,190,9,25
+Post_Nat._Raisin_Bran,120,11,1,6,260,3,200,14,25
+Raisin_Bran,120,14,1,5,240,3,210,12,25
+Almond_Delight,110,14,2,1,-1,2,200,8,25
+Apple_Cinnamon_Cheerios,110,null,2,null,70,2,180,10,25
+Apple_Jacks,110,11,0,1,30,2,125,14,25
+Cheerios,110,17,2,2,105,6,290,1,25
+Clusters,110,13,2,2,105,3,140,7,25
+Cocoa_Puffs,110,12,1,0,55,1,180,13,25
+Corn_Chex,110,22,0,0,25,2,280,3,25
+Corn_Pops,110,13,0,1,20,1,90,12,25
+Count_Chocula,110,12,1,0,65,1,180,13,25
+Cracklin'_Oat_Bran,110,10,3,4,160,3,140,7,25
+Crispix,110,21,0,1,30,2,220,3,25
+Froot_Loops,110,11,1,1,30,2,125,13,25
+Frosted_Flakes,110,14,0,1,25,1,200,11,25
+Fruity_Pebbles,110,13,1,0,25,1,135,12,25
+Golden_Grahams,110,15,1,0,45,1,280,9,25
+Grape-Nuts,110,17,0,3,90,3,170,3,25
+Honey-comb,110,14,0,0,35,1,180,11,25
+Honey_Nut_Cheerios,110,null,1,null,90,3,250,10,25
+Just_Right_Crunchy__Nuggets,110,17,1,1,60,2,170,6,100
+Kix,110,21,1,0,40,2,260,3,25
+Lucky_Charms,110,12,1,0,55,2,180,12,25
+Rice_Chex,110,23,0,0,30,1,240,2,25
+Rice_Krispies,110,22,0,0,35,2,290,3,25
+Smacks,110,9,1,1,40,2,70,15,25
+Special_K,110,16,0,1,55,6,230,3,25
+Total_Corn_Flakes,110,21,1,0,35,2,200,3,100
+Triples,110,21,1,0,60,2,250,3,25
+Trix,110,13,1,0,25,1,140,12,25
+Wheaties_Honey_Gold,110,16,1,1,60,2,200,8,25
+Corn_Flakes,100,21,0,1,35,2,290,2,25
+Cream_of_Wheat_(Quick),100,21,0,1,-1,3,80,0,0
+Crispy_Wheat_&_Raisins,100,11,1,2,120,2,140,10,25
+Double_Chex,100,18,0,1,80,2,190,5,25
+Frosted_Mini-Wheats,100,14,0,3,100,3,0,7,25
+Golden_Crisp,100,11,0,0,40,2,45,15,25
+Grape_Nuts_Flakes,100,15,1,3,85,3,140,5,25
+Life,100,12,2,2,95,4,150,6,25
+Maypo,100,16,1,0,95,4,0,3,25
+Multi-Grain_Cheerios,100,15,1,2,90,2,220,6,25
+Product_19,100,20,0,1,45,3,320,3,100
+Quaker_Oat_Squares,100,14,1,2,110,4,135,6,25
+Quaker_Oatmeal,100,-1,2,null,110,5,0,-1,0
+Raisin_Nut_Bran,100,null,2,null,140,3,140,8,25
+Total_Whole_Grain,100,16,1,3,110,3,200,3,100
+Wheat_Chex,100,17,1,3,115,3,230,3,25
+Wheaties,100,17,1,3,110,3,200,3,25
+Bran_Chex,90,15,1,4,125,2,200,6,25
+Bran_Flakes,90,13,0,5,190,3,210,5,25
+Nutri-grain_Wheat,90,18,0,3,90,3,170,2,25
+Raisin_Squares,90,15,0,2,110,2,0,6,25
+Shredded_Wheat_'n'Bran,90,19,0,4,140,3,0,0,0
+Shredded_Wheat_spoon_size,90,20,0,3,120,3,0,0,0
+Strawberry_Fruit_Wheats,90,15,0,3,90,2,15,5,25
+Shredded_Wheat,80,16,0,3,95,2,0,0,0
+100%_Bran,70,5,1,10,280,4,130,6,25
+All-Bran,70,7,1,9,320,4,260,5,25
+All-Bran_with_Extra_Fiber,50,8,0,14,330,4,140,0,25
+Puffed_Rice,50,13,0,0,15,1,0,0,0
+Puffed_Wheat,50,10,0,1,50,2,0,0,0

package/package.json

@@ -2,7 +2,7 @@
   "name": "@datagrok/bio",
   "beta": false,
   "friendlyName": "Bio",
-  "version": "1.7.5",
+  "version": "1.7.8",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -11,7 +11,7 @@
   },
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "2.8.3",
+    "@datagrok-libraries/bio": "^2.8.4",
     "@datagrok-libraries/utils": "^1.0.0",
     "@datagrok-libraries/ml": "^2.0.10",
     "cash-dom": "latest",

package/src/__jest__/remote.test.ts

@@ -5,7 +5,7 @@
 import * as utils from './test-node';
 import puppeteer from 'puppeteer';
 
-const P_START_TIMEOUT: number = 100000;
+const P_START_TIMEOUT: number = 500000;
 let browser: puppeteer.Browser;
 let page: puppeteer.Page;
 
@@ -16,15 +16,30 @@ beforeAll(async () => {
 }, P_START_TIMEOUT);
 
 afterAll(async () => {
-  await browser.close();
+  await browser?.close();
+});
+
+expect.extend({
+  checkOutput(received, expected, context) {
+    if (received === expected) {
+      return {
+        message: () => context,
+        pass: true
+      };
+    } else {
+      return {
+        message: () => context,
+        pass: false
+      };
+    }
+  }
 });
 
 it('TEST', async () => {
-  const targetPackage: string = process.env.TARGET_PACKAGE ?? 'Bio';
+  const targetPackage:string = process.env.TARGET_PACKAGE ?? 'Bio';
   console.log(`Testing ${targetPackage} package`);
 
-  //console.log(require('root-require')('package.json').version);
-  const r = await page.evaluate((targetPackage): Promise<object> => {
+  const r = await page.evaluate((targetPackage):Promise<object> => {
     return new Promise<object>((resolve, reject) => {
       (<any>window).grok.functions.eval(targetPackage + ':test()').then((df: any) => {
         const cStatus = df.columns.byName('success');
@@ -32,23 +47,22 @@ it('TEST', async () => {
         const cCat = df.columns.byName('category');
         const cName = df.columns.byName('name');
         let failed = false;
-        let report = '';
+        let passReport = '';
+        let failReport = '';
         for (let i = 0; i < df.rowCount; i++) {
-          if (!cStatus.get(i)) {
-            report += `${cCat.get(i)}.${cName.get(i)}: ${cMessage.get(i)}\n`;
+          if (cStatus.get(i)) {
+            passReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+          } else {
             failed = true;
+            failReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
           }
         }
-        resolve({report, failed});
+        resolve({failReport, passReport, failed});
       }).catch((e: any) => reject(e));
     });
   }, targetPackage);
   // @ts-ignore
-  console.log(r.report);
+  console.log(r.passReport);
   // @ts-ignore
-  expect(r.failed).toBe(false);
-}, 100000);
-
-// it('WebLogo.getAlphabetSimilarity', () => {
-//
-// });
+  expect(r.failed).checkOutput(false, r.failReport);
+}, 500000);

package/src/__jest__/test-node.ts

@@ -76,7 +76,7 @@ export async function getBrowserPage(puppeteer: any): Promise<{ browser: any, pa
   await page.goto(url);
   try {
     await page.waitForSelector('.grok-preloader');
-    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 100000});
+    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 500000});
   } catch (error) {
     throw error;
   }

package/src/const.ts

@@ -3,23 +3,23 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
 export const jsonSdfMonomerLibDict = {
-    "monomerType": null, 
-    "smiles": null, 
-    "name": "MonomerName", 
-    "author": null, 
-    "molfile": "molecule", 
-    "naturalAnalog": "MonomerNaturalAnalogCode", 
-    "rgroups": "MonomerCaps",
-    "createDate": null, 
-    "id": null, 
-    "polymerType": "MonomerType", 
-    "symbol": "MonomerCode"
-}
+  'monomerType': null,
+  'smiles': null,
+  'name': 'MonomerName',
+  'author': null,
+  'molfile': 'molecule',
+  'naturalAnalog': 'MonomerNaturalAnalogCode',
+  'rgroups': 'MonomerCaps',
+  'createDate': null,
+  'id': null,
+  'polymerType': 'MonomerType',
+  'symbol': 'MonomerCode'
+};
 
-export const RGROUP_FIELD = "rgroups";
-export const CAP_GROUP_SMILES = "capGroupSmiles";
-export const RGROUP_ALTER_ID = "alternateId";
-export const CAP_GROUP_NAME = "capGroupName";
-export const RGROUP_LABEL = "label";
-export const MONOMER_SYMBOL = "symbol";
-export const SDF_MONOMER_NAME = "MonomerName";
+export const RGROUP_FIELD = 'rgroups';
+export const CAP_GROUP_SMILES = 'capGroupSmiles';
+export const RGROUP_ALTER_ID = 'alternateId';
+export const CAP_GROUP_NAME = 'capGroupName';
+export const RGROUP_LABEL = 'label';
+export const MONOMER_SYMBOL = 'symbol';
+export const SDF_MONOMER_NAME = 'MonomerName';

package/src/package.ts

@@ -208,7 +208,8 @@ export async function multipleSequenceAlignmentAny(table: DG.DataFrame, col: DG.
   if (!checkInputColumn(col, 'MSA', ['fasta'], ['DNA', 'RNA', 'PT']))
     return null;
 
-  const msaCol = await runKalign(col, false);
+  const unUsedName = table.columns.getUnusedName(`msa(${col.name})`);
+  const msaCol = await runKalign(col, false, unUsedName);
   table.columns.add(msaCol);
 
   // This call is required to enable cell renderer activation
@@ -252,7 +253,7 @@ export async function compositionAnalysis(): Promise<void> {
 //name: sdfToJsonLib
 //input: dataframe table
 export async function sdfToJsonLib(table: DG.DataFrame) {
-  const jsonMonomerLibrary = createJsonMonomerLibFromSdf(table);   
+  const jsonMonomerLibrary = createJsonMonomerLibFromSdf(table);
 }
 
 // helper function for importFasta

package/src/tests/convert-test.ts

@@ -83,7 +83,7 @@ MKP---SEYV
 
     separatorGaps: `seq
 F/W//P/H//E/Y
-//Y/N/R/Q/W/Y/V//
+/Y/N/R/Q/W/Y/V/
 M/K/P////S/E/Y/V
 `,
 
@@ -133,6 +133,7 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   }
 
   // FASTA tests
+  // fasta -> separator
   test('testFastaPtToSeparator', async () => {
     await _testConvert(Samples.fastaPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
   });
@@ -142,7 +143,11 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testFastaRnaToSeparator', async () => {
     await _testConvert(Samples.fastaRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
   });
+  test('testFastaGapsToSeparator', async () => {
+    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
+  });
 
+  // fasta -> helm
   test('testFastaPtToHelm', async () => {
     await _testConvert(Samples.fastaPt, converter(NOTATION.HELM), Samples.helmPt);
   });
@@ -152,16 +157,13 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testFastaRnaToHelm', async () => {
     await _testConvert(Samples.fastaRna, converter(NOTATION.HELM), Samples.helmRna);
   });
-
-  test('testFastaGapsToSeparator', async () => {
-    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
-  });
   test('testFastaGapsToHelm', async () => {
-    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR), Samples.helmGaps);
+    await _testConvert(Samples.fastaGaps, converter(NOTATION.HELM), Samples.helmGaps);
   });
 
 
   // SEPARATOR tests
+  // separator -> fasta
   test('testSeparatorPtToFasta', async () => {
     await _testConvert(Samples.separatorPt, converter(NOTATION.FASTA), Samples.fastaPt);
   });
@@ -171,7 +173,11 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testSeparatorRnaToFasta', async () => {
     await _testConvert(Samples.separatorRna, converter(NOTATION.FASTA), Samples.fastaRna);
   });
+  test('testSeparatorGapsToFasta', async () => {
+    await _testConvert(Samples.separatorGaps, converter(NOTATION.FASTA), Samples.fastaGaps);
+  });
 
+  // separator -> helm
   test('testSeparatorPtToHelm', async () => {
     await _testConvert(Samples.separatorPt, converter(NOTATION.HELM), Samples.helmPt);
   });
@@ -181,13 +187,31 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testSeparatorRnaToHelm', async () => {
     await _testConvert(Samples.separatorRna, converter(NOTATION.HELM), Samples.helmRna);
   });
-  test('testSeparatorGapsToFasta', async () => {
-    await _testConvert(Samples.separatorGaps, converter(NOTATION.FASTA), Samples.fastaGaps);
-  });
   test('testSeparatorGapsToHelm', async () => {
     await _testConvert(Samples.separatorGaps, converter(NOTATION.HELM), Samples.helmGaps);
   });
 
 
-  // HELM tests: TODO
+  // HELM tests
+  // helm -> fasta
+  test('HelmDnaToFasta', async () => {
+    await _testConvert(Samples.helmDna, converter(NOTATION.FASTA), Samples.fastaDna);
+  });
+  test('HelmRnaToFasta', async () => {
+    await _testConvert(Samples.helmRna, converter(NOTATION.FASTA), Samples.fastaRna);
+  });
+  test('HelmPtToFasta', async () => {
+    await _testConvert(Samples.helmPt, converter(NOTATION.FASTA), Samples.fastaPt);
+  });
+
+  // helm -> separator
+  test('HelmDnaToSeparator', async () => {
+    await _testConvert(Samples.helmDna, converter(NOTATION.SEPARATOR), Samples.separatorDna);
+  });
+  test('HelmRnaToSeparator', async () => {
+    await _testConvert(Samples.helmRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
+  });
+  test('HelmPtToSeparator', async () => {
+    await _testConvert(Samples.helmPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
+  });
 });