@teselagen/sequence-utils 0.3.24 → 0.3.26

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Files changed (45) hide show
  1. package/calculateNebTm.d.ts +3 -2
  2. package/calculateTm.d.ts +7 -1
  3. package/degenerateDnaToAminoAcidMap.d.ts +1 -1
  4. package/degenerateRnaToAminoAcidMap.d.ts +1 -1
  5. package/getAminoAcidDataForEachBaseOfDna.d.ts +13 -3
  6. package/{index.mjs → index.cjs} +2769 -6273
  7. package/index.d.ts +76 -81
  8. package/index.js +2738 -6242
  9. package/{index.umd.js → index.umd.cjs} +2648 -6152
  10. package/insertSequenceDataAtPosition.d.ts +1 -1
  11. package/package.json +1 -1
  12. package/src/addGapsToSeqReads.js +1 -1
  13. package/src/adjustAnnotationsToInsert.js +1 -1
  14. package/src/autoAnnotate.js +1 -1
  15. package/src/calculateNebTm.js +1 -2
  16. package/src/calculateNebTm.test.js +16 -7
  17. package/src/calculateTm.js +54 -17
  18. package/src/calculateTm.test.js +7 -1
  19. package/src/computeDigestFragments.js +1 -1
  20. package/src/cutSequenceByRestrictionEnzyme.js +1 -1
  21. package/src/degenerateDnaToAminoAcidMap.js +1 -1
  22. package/src/degenerateRnaToAminoAcidMap.js +1 -1
  23. package/src/deleteSequenceDataAtRange.test.js +1 -1
  24. package/src/diffUtils.js +1 -1
  25. package/src/diffUtils.test.js +1 -1
  26. package/src/featureTypesAndColors.js +1 -1
  27. package/src/filterSequenceString.js +1 -1
  28. package/src/findSequenceMatches.js +1 -1
  29. package/src/generateSequenceData.test.js +1 -1
  30. package/src/getAminoAcidDataForEachBaseOfDna.js +246 -115
  31. package/src/getAminoAcidDataForEachBaseOfDna.test.js +55 -0
  32. package/src/getComplementSequenceString.js +1 -1
  33. package/src/getDigestFragmentsForRestrictionEnzymes.js +1 -1
  34. package/src/getReverseComplementAnnotation.js +9 -1
  35. package/src/getReverseComplementSequenceAndAnnotations.js +1 -1
  36. package/src/getReverseComplementSequenceAndAnnotations.test.js +51 -0
  37. package/src/getSequenceDataBetweenRange.js +1 -1
  38. package/src/getVirtualDigest.js +1 -1
  39. package/src/insertSequenceDataAtPositionOrRange.js +1 -1
  40. package/src/insertSequenceDataAtPositionOrRange.test.js +22 -0
  41. package/src/mapAnnotationsToRows.js +1 -1
  42. package/src/prepareCircularViewData.js +1 -1
  43. package/src/rotateSequenceDataToPosition.js +1 -1
  44. package/src/tidyUpAnnotation.js +1 -1
  45. package/src/tidyUpSequenceData.js +9 -2
package/src/tidyUpSequenceData.js CHANGED
@@ -2,12 +2,13 @@
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  import shortid from "shortid";
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  import getAminoAcidDataForEachBaseOfDna from "./getAminoAcidDataForEachBaseOfDna";
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- import { cloneDeep, flatMap } from "lodash";
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+ import { cloneDeep, flatMap } from "lodash-es";
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  import { annotationTypes } from "./annotationTypes";
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  import filterSequenceString from "./filterSequenceString";
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  import tidyUpAnnotation from "./tidyUpAnnotation";
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  import getDegenerateDnaStringFromAaString from "./getDegenerateDnaStringFromAAString";
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  import { getFeatureTypes } from "./featureTypesAndColors";
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+ import getAminoAcidStringFromSequenceString from "./getAminoAcidStringFromSequenceString";
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  export default function tidyUpSequenceData(pSeqData, options = {}) {
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  const {
@@ -16,6 +17,7 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
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  doNotRemoveInvalidChars,
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  additionalValidChars,
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  noTranslationData,
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+ includeProteinSequence,
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  doNotProvideIdsForAnnotations,
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  noCdsTranslations,
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  convertAnnotationsFromAAIndices,
@@ -55,7 +57,8 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
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  if (!doNotRemoveInvalidChars) {
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  if (seqData.isProtein) {
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  const [newSeq] = filterSequenceString(seqData.proteinSequence, {
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- ...(topLevelSeqData || seqData)
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+ ...(topLevelSeqData || seqData),
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+ isProtein: true
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  });
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  seqData.proteinSequence = newSeq;
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  } else {
@@ -79,6 +82,10 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
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  null,
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  true
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  );
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+ } else if (includeProteinSequence) {
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+ seqData.proteinSequence = getAminoAcidStringFromSequenceString(
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+ seqData.sequence
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+ );
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  }
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  seqData.size = seqData.noSequence ? seqData.size : seqData.sequence.length;