@teselagen/sequence-utils 0.1.1

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Files changed (81) hide show
  1. package/DNAComplementMap.d.ts +30 -0
  2. package/addGapsToSeqReads.d.ts +4 -0
  3. package/adjustAnnotationsToInsert.d.ts +1 -0
  4. package/adjustBpsToReplaceOrInsert.d.ts +1 -0
  5. package/aliasedEnzymesByName.d.ts +2 -0
  6. package/aminoAcidToDegenerateDnaMap.d.ts +32 -0
  7. package/aminoAcidToDegenerateRnaMap.d.ts +32 -0
  8. package/annotateSingleSeq.d.ts +7 -0
  9. package/annotationTypes.d.ts +3 -0
  10. package/autoAnnotate.d.ts +8 -0
  11. package/bioData.d.ts +396 -0
  12. package/calculateNebTa.d.ts +4 -0
  13. package/calculateNebTm.d.ts +3 -0
  14. package/calculatePercentGC.d.ts +1 -0
  15. package/calculateTm.d.ts +2 -0
  16. package/computeDigestFragments.d.ts +27 -0
  17. package/condensePairwiseAlignmentDifferences.d.ts +1 -0
  18. package/convertAACaretPositionOrRangeToDna.d.ts +1 -0
  19. package/convertDnaCaretPositionOrRangeToAA.d.ts +1 -0
  20. package/cutSequenceByRestrictionEnzyme.d.ts +1 -0
  21. package/defaultEnzymesByName.d.ts +2 -0
  22. package/degenerateDnaToAminoAcidMap.d.ts +2 -0
  23. package/degenerateRnaToAminoAcidMap.d.ts +2 -0
  24. package/deleteSequenceDataAtRange.d.ts +1 -0
  25. package/diffUtils.d.ts +7 -0
  26. package/doesEnzymeChopOutsideOfRecognitionSite.d.ts +1 -0
  27. package/featureTypesAndColors.d.ts +12 -0
  28. package/filterAminoAcidSequenceString.d.ts +1 -0
  29. package/filterSequenceString.d.ts +1 -0
  30. package/findNearestRangeOfSequenceOverlapToPosition.d.ts +2 -0
  31. package/findOrfsInPlasmid.d.ts +1 -0
  32. package/findSequenceMatches.d.ts +1 -0
  33. package/generateAnnotations.d.ts +2 -0
  34. package/generateSequenceData.d.ts +19 -0
  35. package/getAllInsertionsInSeqReads.d.ts +1 -0
  36. package/getAminoAcidDataForEachBaseOfDna.d.ts +20 -0
  37. package/getAminoAcidFromSequenceTriplet.d.ts +1 -0
  38. package/getAminoAcidStringFromSequenceString.d.ts +1 -0
  39. package/getCodonRangeForAASliver.d.ts +4 -0
  40. package/getComplementAminoAcidStringFromSequenceString.d.ts +1 -0
  41. package/getComplementSequenceAndAnnotations.d.ts +1 -0
  42. package/getComplementSequenceString.d.ts +1 -0
  43. package/getCutsiteType.d.ts +1 -0
  44. package/getCutsitesFromSequence.d.ts +1 -0
  45. package/getDegenerateDnaStringFromAAString.d.ts +1 -0
  46. package/getDegenerateRnaStringFromAAString.d.ts +1 -0
  47. package/getDigestFragmentsForCutsites.d.ts +1 -0
  48. package/getDigestFragmentsForRestrictionEnzymes.d.ts +1 -0
  49. package/getInsertBetweenVals.d.ts +1 -0
  50. package/getLeftAndRightOfSequenceInRangeGivenPosition.d.ts +4 -0
  51. package/getMassOfAaString.d.ts +9 -0
  52. package/getOrfsFromSequence.d.ts +10 -0
  53. package/getOverlapBetweenTwoSequences.d.ts +9 -0
  54. package/getPossiblePartsFromSequenceAndEnzymes.d.ts +1 -0
  55. package/getReverseAminoAcidStringFromSequenceString.d.ts +1 -0
  56. package/getReverseComplementAminoAcidStringFromSequenceString.d.ts +1 -0
  57. package/getReverseComplementAnnotation.d.ts +1 -0
  58. package/getReverseComplementSequenceAndAnnotations.d.ts +1 -0
  59. package/getReverseComplementSequenceString.d.ts +1 -0
  60. package/getReverseSequenceString.d.ts +1 -0
  61. package/getSequenceDataBetweenRange.d.ts +1 -0
  62. package/getVirtualDigest.d.ts +13 -0
  63. package/guessIfSequenceIsDnaAndNotProtein.d.ts +1 -0
  64. package/index.d.ts +85 -0
  65. package/index.js +53 -0
  66. package/index.mjs +17927 -0
  67. package/insertGapsIntoRefSeq.d.ts +1 -0
  68. package/insertSequenceDataAtPosition.d.ts +2 -0
  69. package/insertSequenceDataAtPositionOrRange.d.ts +1 -0
  70. package/isEnzymeType2S.d.ts +1 -0
  71. package/mapAnnotationsToRows.d.ts +3 -0
  72. package/package.json +11 -0
  73. package/prepareCircularViewData.d.ts +1 -0
  74. package/prepareRowData.d.ts +6 -0
  75. package/proteinAlphabet.d.ts +255 -0
  76. package/rotateBpsToPosition.d.ts +1 -0
  77. package/rotateSequenceDataToPosition.d.ts +1 -0
  78. package/shiftAnnotationsByLen.d.ts +5 -0
  79. package/threeLetterSequenceStringToAminoAcidMap.d.ts +898 -0
  80. package/tidyUpAnnotation.d.ts +11 -0
  81. package/tidyUpSequenceData.d.ts +1 -0
package/tidyUpAnnotation.d.ts ADDED
@@ -0,0 +1,11 @@
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+ export default function tidyUpAnnotation(_annotation: any, { sequenceData, convertAnnotationsFromAAIndices, annotationType, provideNewIdsForAnnotations, doNotProvideIdsForAnnotations, messages, mutative, allowNonStandardGenbankTypes, featureTypes }: {
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+ sequenceData?: {} | undefined;
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+ convertAnnotationsFromAAIndices: any;
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+ annotationType: any;
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+ provideNewIdsForAnnotations: any;
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+ doNotProvideIdsForAnnotations: any;
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+ messages?: any[] | undefined;
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+ mutative: any;
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+ allowNonStandardGenbankTypes: any;
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+ featureTypes: any;
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+ }): any;
package/tidyUpSequenceData.d.ts ADDED
@@ -0,0 +1 @@
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+ export default function tidyUpSequenceData(pSeqData: any, options?: {}): any;