@teselagen/sequence-utils 0.3.7 → 0.3.9

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Files changed (108) hide show
  1. package/README.md +89 -0
  2. package/bioData.d.ts +1 -339
  3. package/filterSequenceString.d.ts +26 -1
  4. package/index.d.ts +7 -8
  5. package/index.js +329 -413
  6. package/index.mjs +329 -413
  7. package/index.umd.js +329 -413
  8. package/package.json +1 -2
  9. package/src/addGapsToSeqReads.js +2 -2
  10. package/src/adjustAnnotationsToInsert.js +3 -3
  11. package/src/adjustBpsToReplaceOrInsert.js +3 -3
  12. package/src/adjustBpsToReplaceOrInsert.test.js +0 -1
  13. package/src/aminoAcidToDnaRna.test.js +1 -1
  14. package/src/annotateSingleSeq.js +1 -1
  15. package/src/annotateSingleSeq.test.js +1 -4
  16. package/src/autoAnnotate.js +5 -2
  17. package/src/autoAnnotate.test.js +6 -30
  18. package/src/bioData.js +1 -366
  19. package/src/calculateNebTa.js +1 -1
  20. package/src/calculateNebTm.js +1 -1
  21. package/src/calculatePercentGC.js +2 -2
  22. package/src/calculateTm.js +19 -102
  23. package/src/computeDigestFragments.js +7 -4
  24. package/src/computeDigestFragments.test.js +1 -1
  25. package/src/condensePairwiseAlignmentDifferences.js +1 -1
  26. package/src/convertAACaretPositionOrRangeToDna.js +1 -1
  27. package/src/convertDnaCaretPositionOrRangeToAA.js +1 -1
  28. package/src/cutSequenceByRestrictionEnzyme.js +3 -3
  29. package/src/cutSequenceByRestrictionEnzyme.test.js +0 -1
  30. package/src/degenerateDnaToAminoAcidMap.js +1 -1
  31. package/src/degenerateRnaToAminoAcidMap.js +1 -1
  32. package/src/deleteSequenceDataAtRange.js +1 -1
  33. package/src/deleteSequenceDataAtRange.test.js +23 -9
  34. package/src/diffUtils.js +4 -4
  35. package/src/diffUtils.test.js +2 -2
  36. package/src/doesEnzymeChopOutsideOfRecognitionSite.js +1 -1
  37. package/src/doesEnzymeChopOutsideOfRecognitionSite.test.js +0 -2
  38. package/src/featureTypesAndColors.js +5 -5
  39. package/src/featureTypesAndColors.test.js +1 -1
  40. package/src/filterSequenceString.js +111 -16
  41. package/src/filterSequenceString.test.js +62 -3
  42. package/src/findNearestRangeOfSequenceOverlapToPosition.js +1 -1
  43. package/src/findOrfsInPlasmid.js +1 -1
  44. package/src/findSequenceMatches.js +9 -10
  45. package/src/generateAnnotations.js +1 -1
  46. package/src/generateSequenceData.js +1 -1
  47. package/src/generateSequenceData.test.js +1 -1
  48. package/src/getAllInsertionsInSeqReads.js +1 -1
  49. package/src/getAminoAcidDataForEachBaseOfDna.js +2 -2
  50. package/src/getAminoAcidDataForEachBaseOfDna.test.js +0 -2
  51. package/src/getAminoAcidFromSequenceTriplet.js +1 -1
  52. package/src/getAminoAcidStringFromSequenceString.js +1 -1
  53. package/src/getCodonRangeForAASliver.js +1 -1
  54. package/src/getComplementAminoAcidStringFromSequenceString.js +2 -5
  55. package/src/getComplementSequenceAndAnnotations.js +1 -2
  56. package/src/getComplementSequenceString.js +5 -3
  57. package/src/getComplementSequenceString.test.js +6 -6
  58. package/src/getCutsiteType.js +1 -1
  59. package/src/getCutsitesFromSequence.js +1 -1
  60. package/src/getDegenerateDnaStringFromAAString.js +1 -1
  61. package/src/getDegenerateRnaStringFromAAString.js +1 -1
  62. package/src/getDigestFragmentsForCutsites.js +5 -2
  63. package/src/getDigestFragmentsForRestrictionEnzymes.js +2 -2
  64. package/src/getInsertBetweenVals.js +2 -2
  65. package/src/getLeftAndRightOfSequenceInRangeGivenPosition.js +2 -2
  66. package/src/getLeftAndRightOfSequenceInRangeGivenPosition.test.js +0 -2
  67. package/src/getMassOfAaString.js +4 -1
  68. package/src/getMassofAaString.test.js +9 -8
  69. package/src/getOrfsFromSequence.js +1 -2
  70. package/src/getOrfsFromSequence.test.js +1 -3
  71. package/src/getOverlapBetweenTwoSequences.js +3 -3
  72. package/src/getOverlapBetweenTwoSequences.test.js +1 -1
  73. package/src/getPossiblePartsFromSequenceAndEnzymes.js +2 -2
  74. package/src/getReverseAminoAcidStringFromSequenceString.js +1 -1
  75. package/src/getReverseComplementAminoAcidStringFromSequenceString.js +9 -6
  76. package/src/getReverseComplementAnnotation.js +1 -1
  77. package/src/getReverseComplementSequenceAndAnnotations.js +2 -3
  78. package/src/getReverseComplementSequenceString.js +1 -2
  79. package/src/getReverseSequenceString.js +1 -1
  80. package/src/getSequenceDataBetweenRange.js +7 -4
  81. package/src/getSequenceDataBetweenRange.test.js +0 -1
  82. package/src/getVirtualDigest.js +6 -3
  83. package/src/guessIfSequenceIsDnaAndNotProtein.js +2 -2
  84. package/src/index.js +79 -80
  85. package/src/index.test.js +5 -4
  86. package/src/insertGapsIntoRefSeq.js +1 -1
  87. package/src/insertSequenceDataAtPosition.test.js +4 -2
  88. package/src/insertSequenceDataAtPositionOrRange.js +5 -5
  89. package/src/insertSequenceDataAtPositionOrRange.test.js +3 -17
  90. package/src/isEnzymeType2S.js +1 -1
  91. package/src/mapAnnotationsToRows.js +3 -3
  92. package/src/mapAnnotationsToRows.test.js +1 -3
  93. package/src/prepareCircularViewData.js +5 -5
  94. package/src/prepareCircularViewData.test.js +1 -1
  95. package/src/prepareRowData.js +1 -2
  96. package/src/prepareRowData.test.js +1 -3
  97. package/src/prepareRowData_output1.json +381 -381
  98. package/src/proteinAlphabet.js +31 -26
  99. package/src/rotateBpsToPosition.js +7 -11
  100. package/src/rotateBpsToPosition.test.js +6 -6
  101. package/src/rotateSequenceDataToPosition.js +4 -4
  102. package/src/shiftAnnotationsByLen.js +2 -2
  103. package/src/tidyUpAnnotation.js +8 -7
  104. package/src/tidyUpSequenceData.js +15 -18
  105. package/filterAminoAcidSequenceString.d.ts +0 -1
  106. package/filterAminoAcidSequenceString.test.d.ts +0 -1
  107. package/src/filterAminoAcidSequenceString.js +0 -13
  108. package/src/filterAminoAcidSequenceString.test.js +0 -22
@@ -1,12 +1,12 @@
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- import { cloneDeep } from 'lodash';
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- import { getYOffsetsForPotentiallyCircularRanges } from '@teselagen/range-utils';
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- import { annotationTypes } from './annotationTypes';
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+ import { cloneDeep } from "lodash";
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+ import { getYOffsetsForPotentiallyCircularRanges } from "@teselagen/range-utils";
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+ import { annotationTypes } from "./annotationTypes";
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4
 
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  //basically just adds yOffsets to the annotations
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  export default function prepareCircularViewData(sequenceData) {
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  const clonedSeqData = cloneDeep(sequenceData);
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- annotationTypes.forEach((annotationType) => {
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- if (annotationType !== 'cutsites') {
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+ annotationTypes.forEach(annotationType => {
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+ if (annotationType !== "cutsites") {
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  const maxYOffset = getYOffsetsForPotentiallyCircularRanges(
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  clonedSeqData[annotationType]
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  ).maxYOffset;
@@ -1,4 +1,4 @@
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- import {expect} from "chai";
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+ import { expect } from "chai";
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  import mapAnnotationsToRows from "./mapAnnotationsToRows.js";
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  describe("prepareCircularViewData", () => {
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  it("maps overlapping annotations to rows correctly", () => {
@@ -1,4 +1,3 @@
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-
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  // ac.throw([ac.posInt, ac.posInt, ac.bool], arguments);
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  import mapAnnotationsToRows from "./mapAnnotationsToRows";
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3
 
@@ -38,4 +37,4 @@ export default function prepareRowData(sequenceData, bpsPerRow) {
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  rows[rowNumber] = row;
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  }
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  return rows;
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- };
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+ }
@@ -1,6 +1,4 @@
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-
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-
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- import {expect} from "chai";
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+ import { expect } from "chai";
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2
 
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  import prepareRowData from "./prepareRowData";
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  import output1 from "./prepareRowData_output1.json";