@datagrok/bio 2.1.7 → 2.1.9

package/files/tests/SPGI-derived.csv

@@ -0,0 +1,320 @@
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package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.1.7",
+  "version": "2.1.9",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",

package/src/package.ts

@@ -588,9 +588,6 @@ export async function testDetectMacromolecule(path: string): Promise<DG.DataFram
 //tags: panel, bio
 //input: column col {semType: Macromolecule}
 export function splitToMonomers(col: DG.Column<string>): void {
-  if (!col.getTag(bio_TAGS.aligned).includes(C.MSA))
-    return grok.shell.error('Splitting is applicable only for aligned sequences');
-
   const tempDf = splitAlignedSequences(col);
   const originalDf = col.dataFrame;
   for (const tempCol of tempDf.columns) {

package/src/tests/detectors-tests.ts

@@ -7,6 +7,17 @@ import {after, before, category, test, expect, expectObject} from '@datagrok-lib
 
 import {importFasta} from '../package';
 
+/*
+// snippet to list df columns of semType='Macromolecule' (false positive)
+const df = grok.shell.tableByName('SPGI');
+for (let i = 0; i < df.columns.length; i++) {
+  const col = df.columns.byIndex(i);
+  if (col.semType == 'Macromolecule') {
+  console.log( i + ' - ' + col.name + ' - ' + col.semType);
+  }
+}
+ */
+
 type DfReaderFunc = () => Promise<DG.DataFrame>;
 
 category('detectors', () => {
@@ -127,6 +138,7 @@ MWRSWY-CKHP
     testUnichemSources = 'testUnichemSources',
     testDmvOffices = 'testDmvOffices',
     testAlertCollection = 'testAlertCollection',
+    testSpgi = 'testSpgi',
   }
 
   const samples: { [key: string]: string } = {
@@ -148,6 +160,7 @@ MWRSWY-CKHP
     [Samples.testUnichemSources]: 'System:AppData/Bio/tests/testUnichemSources.csv',
     [Samples.testDmvOffices]: 'System:AppData/Bio/tests/testDmvOffices.csv',
     [Samples.testAlertCollection]: 'System:AppData/Bio/tests/testAlertCollection.csv',
+    [Samples.testSpgi]: 'System:AppData/Bio/tests/SPGI-derived.csv',
   };
 
   const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
@@ -337,7 +350,8 @@ MWRSWY-CKHP
   });
 
   test('samplesFastaPtPosSequence', async () => {
-    await _testPos(readSamples(Samples.fastaPtCsv), 'sequence', bio.NOTATION.FASTA, bio.ALIGNMENT.SEQ, bio.ALPHABET.PT, 20, false);
+    await _testPos(readSamples(Samples.fastaPtCsv), 'sequence',
+      bio.NOTATION.FASTA, bio.ALIGNMENT.SEQ, bio.ALPHABET.PT, 20, false);
   });
 
   test('samplesTestCerealNegativeCerealName', async () => {
@@ -374,6 +388,10 @@ MWRSWY-CKHP
   test('samplesTestAlertCollectionNegativeSmarts', async () => {
     await _testNeg(readSamples(Samples.testAlertCollection), 'smarts');
   });
+
+  test('samplesTestSpgiNegativeVals', async () => {
+    await _testNeg(readSamples(Samples.testSpgi), 'vals');
+  });
 });
 
 export async function _testNeg(readDf: DfReaderFunc, colName: string) {

package/{test-Bio-62cc009524f3-6c978eb5.html → test-Bio-62cc009524f3-820f73b0.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 6c978eb5.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 820f73b0.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 6c978eb5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-17 12:14:47</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">41.993s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">30.068s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 820f73b0.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-21 17:50:27</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">51.915s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">35.984s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:40:11
@@ -244,120 +244,121 @@ header {
     at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
     at runMicrotasks (&lt;anonymous&gt;)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
-Test result : Success : 13 : Bio.Palettes.testPaletteAA : OK
-Test result : Success : 1 : Bio.Palettes.testPalettePtMe : OK
-Test result : Success : 120 : Bio.detectors.NegativeEmpty : OK
-Test result : Success : 37 : Bio.detectors.Negative1 : OK
-Test result : Success : 48 : Bio.detectors.Negative2 : OK
-Test result : Success : 47 : Bio.detectors.Negative3 : OK
-Test result : Success : 451 : Bio.detectors.NegativeSmiles : OK
-Test result : Success : 32 : Bio.detectors.Dna1 : OK
-Test result : Success : 26 : Bio.detectors.Rna1 : OK
-Test result : Success : 25 : Bio.detectors.AA1 : OK
-Test result : Success : 20 : Bio.detectors.MsaDna1 : OK
-Test result : Success : 19 : Bio.detectors.MsaAA1 : OK
-Test result : Success : 10 : Bio.detectors.SepDna : OK
-Test result : Success : 22 : Bio.detectors.SepRna : OK
-Test result : Success : 25 : Bio.detectors.SepPt : OK
-Test result : Success : 12 : Bio.detectors.SepUn1 : OK
-Test result : Success : 18 : Bio.detectors.SepUn2 : OK
-Test result : Success : 30 : Bio.detectors.SepMsaN1 : OK
-Test result : Success : 459 : Bio.detectors.SamplesFastaCsvPt : OK
-Test result : Success : 23 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
-Test result : Success : 6 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
-Test result : Success : 35 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
-Test result : Success : 426 : Bio.detectors.SamplesFastaFastaPt : OK
-Test result : Success : 1008 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
-Test result : Success : 28 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
-Test result : Success : 31 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
-Test result : Success : 292 : Bio.detectors.samplesMsaComplexUn : OK
-Test result : Success : 19 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
-Test result : Success : 239 : Bio.detectors.samplesIdCsvNegativeID : OK
-Test result : Success : 150 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
-Test result : Success : 192 : Bio.detectors.samplesHelmCsvHELM : OK
-Test result : Success : 14 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
-Test result : Success : 155 : Bio.detectors.samplesTestHelmNegativeID : OK
-Test result : Success : 19 : Bio.detectors.samplesTestHelmNegativeTestType : OK
-Test result : Success : 21 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
-Test result : Success : 24 : Bio.detectors.samplesTestHelmNegativeValid : OK
-Test result : Success : 16 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
-Test result : Success : 11 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
-Test result : Success : 17 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
-Test result : Success : 927 : Bio.detectors.samplesTestDemogNegativeAll : OK
-Test result : Success : 260 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
-Test result : Success : 144 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
-Test result : Success : 118 : Bio.detectors.samplesFastaPtPosSequence : OK
-Test result : Success : 119 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
-Test result : Success : 189 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
-Test result : Success : 6 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
-Test result : Success : 8 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
-Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
-Test result : Success : 122 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
+Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
+Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
+Test result : Success : 266 : Bio.detectors.NegativeEmpty : OK
+Test result : Success : 46 : Bio.detectors.Negative1 : OK
+Test result : Success : 76 : Bio.detectors.Negative2 : OK
+Test result : Success : 25 : Bio.detectors.Negative3 : OK
+Test result : Success : 647 : Bio.detectors.NegativeSmiles : OK
+Test result : Success : 64 : Bio.detectors.Dna1 : OK
+Test result : Success : 24 : Bio.detectors.Rna1 : OK
+Test result : Success : 23 : Bio.detectors.AA1 : OK
+Test result : Success : 17 : Bio.detectors.MsaDna1 : OK
+Test result : Success : 34 : Bio.detectors.MsaAA1 : OK
+Test result : Success : 23 : Bio.detectors.SepDna : OK
+Test result : Success : 24 : Bio.detectors.SepRna : OK
+Test result : Success : 24 : Bio.detectors.SepPt : OK
+Test result : Success : 32 : Bio.detectors.SepUn1 : OK
+Test result : Success : 41 : Bio.detectors.SepUn2 : OK
+Test result : Success : 33 : Bio.detectors.SepMsaN1 : OK
+Test result : Success : 750 : Bio.detectors.SamplesFastaCsvPt : OK
+Test result : Success : 17 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
+Test result : Success : 16 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
+Test result : Success : 41 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
+Test result : Success : 347 : Bio.detectors.SamplesFastaFastaPt : OK
+Test result : Success : 1222 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
+Test result : Success : 43 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
+Test result : Success : 20 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
+Test result : Success : 300 : Bio.detectors.samplesMsaComplexUn : OK
+Test result : Success : 7 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
+Test result : Success : 191 : Bio.detectors.samplesIdCsvNegativeID : OK
+Test result : Success : 172 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
+Test result : Success : 168 : Bio.detectors.samplesHelmCsvHELM : OK
+Test result : Success : 9 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
+Test result : Success : 180 : Bio.detectors.samplesTestHelmNegativeID : OK
+Test result : Success : 32 : Bio.detectors.samplesTestHelmNegativeTestType : OK
+Test result : Success : 26 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
+Test result : Success : 20 : Bio.detectors.samplesTestHelmNegativeValid : OK
+Test result : Success : 7 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
+Test result : Success : 39 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
+Test result : Success : 16 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
+Test result : Success : 1164 : Bio.detectors.samplesTestDemogNegativeAll : OK
+Test result : Success : 366 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
+Test result : Success : 183 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
+Test result : Success : 149 : Bio.detectors.samplesFastaPtPosSequence : OK
+Test result : Success : 141 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
+Test result : Success : 228 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
+Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
+Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
+Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
+Test result : Success : 190 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
 Test result : Success : 5 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
-Test result : Success : 125 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
+Test result : Success : 158 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
 Test result : Success : 10 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
-Test result : Success : 140 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
-Test result : Success : 6 : Bio.detectorsBenchmark.separatorDnaShorts50Few50 : OK
-Test result : Success : 8636 : Bio.detectorsBenchmark.separatorDnaShorts50Many1E6 : OK
-Test result : Success : 1248 : Bio.MSA.isCorrect : OK
-Test result : Success : 114 : Bio.MSA.isCorrectLong : OK
-Test result : Success : 998 : Bio.sequenceSpace.sequenceSpaceOpens : OK
-Test result : Success : 462 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
-Test result : Success : 749 : Bio.activityCliffs.activityCliffsOpens : OK
-Test result : Success : 824 : Bio.activityCliffs.activityCliffsWithEmptyRows : OK
-Test result : Success : 0 : Bio.splitters.fastaMulti : OK
+Test result : Success : 300 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
+Test result : Success : 140 : Bio.detectors.samplesTestSpgiNegativeVals : OK
+Test result : Success : 12 : Bio.detectorsBenchmark.separatorDnaShorts50Few50 : OK
+Test result : Success : 10234 : Bio.detectorsBenchmark.separatorDnaShorts50Many1E6 : OK
+Test result : Success : 1702 : Bio.MSA.isCorrect : OK
+Test result : Success : 95 : Bio.MSA.isCorrectLong : OK
+Test result : Success : 1274 : Bio.sequenceSpace.sequenceSpaceOpens : OK
+Test result : Success : 609 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
+Test result : Success : 934 : Bio.activityCliffs.activityCliffsOpens : OK
+Test result : Success : 1024 : Bio.activityCliffs.activityCliffsWithEmptyRows : OK
+Test result : Success : 1 : Bio.splitters.fastaMulti : OK
 Test result : Success : 1 : Bio.splitters.helm1 : OK
-Test result : Success : 0 : Bio.splitters.helm2 : OK
-Test result : Success : 0 : Bio.splitters.helm3-multichar : OK
+Test result : Success : 1 : Bio.splitters.helm2 : OK
+Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
 Test result : Success : 0 : Bio.splitters.testHelm1 : OK
 Test result : Success : 1 : Bio.splitters.testHelm2 : OK
 Test result : Success : 0 : Bio.splitters.testHelm3 : OK
-Test result : Success : 285 : Bio.splitters.splitToMonomers : OK
+Test result : Success : 352 : Bio.splitters.splitToMonomers : OK
 Test result : Success : 2 : Bio.splitters.getHelmMonomers : OK
-Test result : Success : 70 : Bio.renderers.long sequence performance  : OK
-Test result : Success : 841 : Bio.renderers.many sequence performance : OK
-Test result : Success : 290 : Bio.renderers.rendererMacromoleculeFasta : OK
-Test result : Success : 233 : Bio.renderers.rendererMacromoleculeSeparator : OK
-Test result : Success : 98 : Bio.renderers.rendererMacromoleculeDifference : OK
-Test result : Success : 400 : Bio.renderers.afterMsa : OK
-Test result : Success : 241 : Bio.renderers.afterConvert : OK
-Test result : Success : 173 : Bio.renderers.selectRendererBySemType : OK
-Test result : Success : 7 : Bio.converters.testFastaPtToSeparator : OK
-Test result : Success : 5 : Bio.converters.testFastaDnaToSeparator : OK
-Test result : Success : 5 : Bio.converters.testFastaRnaToSeparator : OK
-Test result : Success : 4 : Bio.converters.testFastaGapsToSeparator : OK
-Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
-Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
-Test result : Success : 2 : Bio.converters.testFastaRnaToHelm : OK
-Test result : Success : 2 : Bio.converters.testFastaGapsToHelm : OK
-Test result : Success : 0 : Bio.converters.testSeparatorPtToFasta : OK
+Test result : Success : 92 : Bio.renderers.long sequence performance  : OK
+Test result : Success : 964 : Bio.renderers.many sequence performance : OK
+Test result : Success : 367 : Bio.renderers.rendererMacromoleculeFasta : OK
+Test result : Success : 254 : Bio.renderers.rendererMacromoleculeSeparator : OK
+Test result : Success : 97 : Bio.renderers.rendererMacromoleculeDifference : OK
+Test result : Success : 554 : Bio.renderers.afterMsa : OK
+Test result : Success : 389 : Bio.renderers.afterConvert : OK
+Test result : Success : 215 : Bio.renderers.selectRendererBySemType : OK
+Test result : Success : 8 : Bio.converters.testFastaPtToSeparator : OK
+Test result : Success : 7 : Bio.converters.testFastaDnaToSeparator : OK
+Test result : Success : 6 : Bio.converters.testFastaRnaToSeparator : OK
+Test result : Success : 6 : Bio.converters.testFastaGapsToSeparator : OK
+Test result : Success : 4 : Bio.converters.testFastaPtToHelm : OK
+Test result : Success : 3 : Bio.converters.testFastaDnaToHelm : OK
+Test result : Success : 4 : Bio.converters.testFastaRnaToHelm : OK
+Test result : Success : 11 : Bio.converters.testFastaGapsToHelm : OK
+Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
 Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
-Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
+Test result : Success : 1 : Bio.converters.testSeparatorRnaToFasta : OK
 Test result : Success : 1 : Bio.converters.testSeparatorGapsToFasta : OK
-Test result : Success : 0 : Bio.converters.testSeparatorPtToHelm : OK
+Test result : Success : 1 : Bio.converters.testSeparatorPtToHelm : OK
 Test result : Success : 1 : Bio.converters.testSeparatorDnaToHelm : OK
-Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
-Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
-Test result : Success : 0 : Bio.converters.testHelmDnaToFasta : OK
-Test result : Success : 0 : Bio.converters.testHelmRnaToFasta : OK
+Test result : Success : 1 : Bio.converters.testSeparatorRnaToHelm : OK
+Test result : Success : 1 : Bio.converters.testSeparatorGapsToHelm : OK
+Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
+Test result : Success : 1 : Bio.converters.testHelmRnaToFasta : OK
 Test result : Success : 1 : Bio.converters.testHelmPtToFasta : OK
 Test result : Success : 1 : Bio.converters.testHelmDnaToSeparator : OK
 Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
-Test result : Success : 1 : Bio.converters.testHelmPtToSeparator : OK
-Test result : Success : 1 : Bio.converters.testHelmLoneRibose : OK
-Test result : Success : 1 : Bio.converters.testHelmLoneDeoxyribose : OK
-Test result : Success : 1 : Bio.converters.testHelmLonePhosphorus : OK
-Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
+Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
+Test result : Success : 4 : Bio.converters.testHelmLoneRibose : OK
+Test result : Success : 2 : Bio.converters.testHelmLoneDeoxyribose : OK
+Test result : Success : 4 : Bio.converters.testHelmLonePhosphorus : OK
+Test result : Success : 1 : Bio.fastaFileHandler.testNormalFormatting : OK
 Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
-Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
-Test result : Success : 1 : Bio.fastaExport.wrapSequenceSingle : OK
-Test result : Success : 0 : Bio.fastaExport.wrapSequenceMulti : OK
-Test result : Success : 2 : Bio.fastaExport.saveAsFastaTest1 : OK
+Test result : Success : 1 : Bio.fastaFileHandler.testExtraNewlines : OK
+Test result : Success : 0 : Bio.fastaExport.wrapSequenceSingle : OK
+Test result : Success : 1 : Bio.fastaExport.wrapSequenceMulti : OK
+Test result : Success : 1 : Bio.fastaExport.saveAsFastaTest1 : OK
 Test result : Success : 1 : Bio.fastaExport.saveAsFastaTest2 : OK
 Test result : Success : 1 : Bio.bio.testGetStatsHelm1 : OK
 Test result : Success : 1 : Bio.bio.testGetStatsN1 : OK
 Test result : Success : 0 : Bio.bio.testGetAlphabetSimilarity : OK
-Test result : Success : 1 : Bio.bio.testPickupPaletteN1 : OK
+Test result : Success : 2 : Bio.bio.testPickupPaletteN1 : OK
 Test result : Success : 1 : Bio.bio.testPickupPaletteN1e : OK
 Test result : Success : 1 : Bio.bio.testPickupPaletteAA1 : OK
 Test result : Success : 1 : Bio.bio.testPickupPaletteX : OK
@@ -366,17 +367,17 @@ Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerShort : OK
 Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
 Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartShort : OK
 Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartLong56 : OK
-Test result : Success : 102 : Bio.WebLogo-positions.allPositions : OK
-Test result : Success : 86 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
-Test result : Success : 88 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
-Test result : Success : 3 : Bio.checkInputColumn.testMsaPos : OK
+Test result : Success : 133 : Bio.WebLogo-positions.allPositions : OK
+Test result : Success : 139 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
+Test result : Success : 119 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
+Test result : Success : 4 : Bio.checkInputColumn.testMsaPos : OK
 Test result : Success : 1 : Bio.checkInputColumn.testMsaNegHelm : OK
 Test result : Success : 1 : Bio.checkInputColumn.testMsaNegUN : OK
 Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
-Test result : Success : 427 : Bio.similarity/diversity.similaritySearchViewer : OK
-Test result : Success : 527 : Bio.similarity/diversity.diversitySearchViewer : OK
-Test result : Success : 216 : Bio.substructureFilters.fasta : OK
-Test result : Success : 435 : Bio.substructureFilters.separator : OK
+Test result : Success : 493 : Bio.similarity/diversity.similaritySearchViewer : OK
+Test result : Success : 337 : Bio.similarity/diversity.diversitySearchViewer : OK
+Test result : Success : 242 : Bio.substructureFilters.fasta : OK
+Test result : Success : 425 : Bio.substructureFilters.separator : OK
 </pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:74:11
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)