@teselagen/sequence-utils 0.3.38-beta.3 → 0.3.42

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Files changed (172) hide show
  1. package/DNAComplementMap.d.ts +1 -1
  2. package/README.md +2 -8
  3. package/addGapsToSeqReads.d.ts +3 -16
  4. package/adjustAnnotationsToInsert.d.ts +1 -2
  5. package/adjustBpsToReplaceOrInsert.d.ts +1 -2
  6. package/aliasedEnzymesByName.d.ts +1 -37
  7. package/aminoAcidToDegenerateDnaMap.d.ts +31 -1
  8. package/aminoAcidToDegenerateRnaMap.d.ts +1 -1
  9. package/annotateSingleSeq.d.ts +4 -5
  10. package/annotationTypes.d.ts +2 -2
  11. package/autoAnnotate.d.ts +8 -17
  12. package/bioData.d.ts +58 -10
  13. package/calculateEndStability.d.ts +1 -1
  14. package/calculateNebTa.d.ts +1 -6
  15. package/calculateNebTm.d.ts +4 -6
  16. package/calculatePercentGC.d.ts +1 -1
  17. package/calculateSantaLuciaTm.d.ts +114 -28
  18. package/calculateTm.d.ts +1 -13
  19. package/computeDigestFragments.d.ts +24 -30
  20. package/condensePairwiseAlignmentDifferences.d.ts +1 -1
  21. package/convertAACaretPositionOrRangeToDna.d.ts +1 -2
  22. package/convertDnaCaretPositionOrRangeToAA.d.ts +1 -2
  23. package/cutSequenceByRestrictionEnzyme.d.ts +1 -2
  24. package/defaultEnzymesByName.d.ts +1 -2
  25. package/degenerateDnaToAminoAcidMap.d.ts +1 -1
  26. package/degenerateRnaToAminoAcidMap.d.ts +1 -1
  27. package/deleteSequenceDataAtRange.d.ts +1 -2
  28. package/diffUtils.d.ts +7 -9
  29. package/doesEnzymeChopOutsideOfRecognitionSite.d.ts +1 -2
  30. package/featureTypesAndColors.d.ts +6 -19
  31. package/filterSequenceString.d.ts +10 -14
  32. package/findApproxMatches.d.ts +1 -7
  33. package/findNearestRangeOfSequenceOverlapToPosition.d.ts +1 -2
  34. package/findOrfsInPlasmid.d.ts +11 -2
  35. package/findSequenceMatches.d.ts +1 -11
  36. package/generateAnnotations.d.ts +1 -2
  37. package/generateSequenceData.d.ts +13 -8
  38. package/getAllInsertionsInSeqReads.d.ts +1 -11
  39. package/getAminoAcidDataForEachBaseOfDna.d.ts +5 -6
  40. package/getAminoAcidFromSequenceTriplet.d.ts +1 -1
  41. package/getAminoAcidStringFromSequenceString.d.ts +1 -3
  42. package/getCodonRangeForAASliver.d.ts +4 -3
  43. package/getComplementAminoAcidStringFromSequenceString.d.ts +1 -1
  44. package/getComplementSequenceAndAnnotations.d.ts +1 -5
  45. package/getComplementSequenceString.d.ts +1 -1
  46. package/getCutsiteType.d.ts +1 -2
  47. package/getCutsitesFromSequence.d.ts +1 -2
  48. package/getDegenerateDnaStringFromAAString.d.ts +1 -1
  49. package/getDegenerateRnaStringFromAAString.d.ts +1 -1
  50. package/getDigestFragmentsForCutsites.d.ts +1 -4
  51. package/getDigestFragmentsForRestrictionEnzymes.d.ts +1 -8
  52. package/getInsertBetweenVals.d.ts +1 -2
  53. package/getLeftAndRightOfSequenceInRangeGivenPosition.d.ts +1 -2
  54. package/getOrfsFromSequence.d.ts +11 -17
  55. package/getOverlapBetweenTwoSequences.d.ts +1 -2
  56. package/getPossiblePartsFromSequenceAndEnzymes.d.ts +1 -18
  57. package/getReverseAminoAcidStringFromSequenceString.d.ts +1 -1
  58. package/getReverseComplementAminoAcidStringFromSequenceString.d.ts +1 -1
  59. package/getReverseComplementAnnotation.d.ts +1 -11
  60. package/getReverseComplementSequenceAndAnnotations.d.ts +1 -5
  61. package/getReverseComplementSequenceString.d.ts +1 -1
  62. package/getReverseSequenceString.d.ts +1 -1
  63. package/getSequenceDataBetweenRange.d.ts +1 -9
  64. package/getVirtualDigest.d.ts +10 -11
  65. package/guessIfSequenceIsDnaAndNotProtein.d.ts +1 -5
  66. package/index.cjs +503 -734
  67. package/index.d.ts +5 -8
  68. package/index.js +503 -734
  69. package/index.umd.cjs +503 -734
  70. package/insertGapsIntoRefSeq.d.ts +1 -2
  71. package/insertSequenceDataAtPositionOrRange.d.ts +1 -10
  72. package/isEnzymeType2S.d.ts +1 -2
  73. package/mapAnnotationsToRows.d.ts +1 -9
  74. package/package.json +9 -12
  75. package/prepareCircularViewData.d.ts +1 -2
  76. package/prepareRowData.d.ts +3 -7
  77. package/proteinAlphabet.d.ts +1 -1
  78. package/rotateBpsToPosition.d.ts +1 -1
  79. package/rotateSequenceDataToPosition.d.ts +1 -3
  80. package/shiftAnnotationsByLen.d.ts +3 -4
  81. package/src/autoAnnotate.test.js +1 -0
  82. package/src/filterSequenceString.js +7 -4
  83. package/src/getSequenceDataBetweenRange.js +11 -2
  84. package/src/getSequenceDataBetweenRange.test.js +42 -0
  85. package/src/prepareRowData_output1.json +0 -1
  86. package/src/tidyUpSequenceData.js +5 -2
  87. package/threeLetterSequenceStringToAminoAcidMap.d.ts +921 -11
  88. package/tidyUpAnnotation.d.ts +11 -13
  89. package/tidyUpSequenceData.d.ts +1 -15
  90. package/src/DNAComplementMap.ts +0 -32
  91. package/src/addGapsToSeqReads.ts +0 -436
  92. package/src/adjustAnnotationsToInsert.ts +0 -20
  93. package/src/adjustBpsToReplaceOrInsert.ts +0 -73
  94. package/src/aliasedEnzymesByName.ts +0 -7366
  95. package/src/aminoAcidToDegenerateDnaMap.ts +0 -32
  96. package/src/aminoAcidToDegenerateRnaMap.ts +0 -32
  97. package/src/annotateSingleSeq.ts +0 -37
  98. package/src/annotationTypes.ts +0 -23
  99. package/src/autoAnnotate.ts +0 -290
  100. package/src/bioData.ts +0 -65
  101. package/src/calculateEndStability.ts +0 -91
  102. package/src/calculateNebTa.ts +0 -46
  103. package/src/calculateNebTm.ts +0 -132
  104. package/src/calculatePercentGC.ts +0 -3
  105. package/src/calculateSantaLuciaTm.ts +0 -184
  106. package/src/calculateTm.ts +0 -242
  107. package/src/computeDigestFragments.ts +0 -238
  108. package/src/condensePairwiseAlignmentDifferences.ts +0 -85
  109. package/src/convertAACaretPositionOrRangeToDna.ts +0 -28
  110. package/src/convertDnaCaretPositionOrRangeToAA.ts +0 -28
  111. package/src/cutSequenceByRestrictionEnzyme.ts +0 -345
  112. package/src/defaultEnzymesByName.ts +0 -280
  113. package/src/degenerateDnaToAminoAcidMap.ts +0 -5
  114. package/src/degenerateRnaToAminoAcidMap.ts +0 -5
  115. package/src/deleteSequenceDataAtRange.ts +0 -13
  116. package/src/diffUtils.ts +0 -80
  117. package/src/doesEnzymeChopOutsideOfRecognitionSite.ts +0 -16
  118. package/src/featureTypesAndColors.ts +0 -167
  119. package/src/filterSequenceString.ts +0 -153
  120. package/src/findApproxMatches.ts +0 -58
  121. package/src/findNearestRangeOfSequenceOverlapToPosition.ts +0 -43
  122. package/src/findOrfsInPlasmid.ts +0 -31
  123. package/src/findSequenceMatches.ts +0 -154
  124. package/src/generateAnnotations.ts +0 -39
  125. package/src/generateSequenceData.ts +0 -212
  126. package/src/getAllInsertionsInSeqReads.ts +0 -100
  127. package/src/getAminoAcidDataForEachBaseOfDna.ts +0 -305
  128. package/src/getAminoAcidFromSequenceTriplet.ts +0 -27
  129. package/src/getAminoAcidStringFromSequenceString.ts +0 -36
  130. package/src/getCodonRangeForAASliver.ts +0 -73
  131. package/src/getComplementAminoAcidStringFromSequenceString.ts +0 -10
  132. package/src/getComplementSequenceAndAnnotations.ts +0 -25
  133. package/src/getComplementSequenceString.ts +0 -23
  134. package/src/getCutsiteType.ts +0 -18
  135. package/src/getCutsitesFromSequence.ts +0 -22
  136. package/src/getDegenerateDnaStringFromAAString.ts +0 -15
  137. package/src/getDegenerateRnaStringFromAAString.ts +0 -15
  138. package/src/getDigestFragmentsForCutsites.ts +0 -126
  139. package/src/getDigestFragmentsForRestrictionEnzymes.ts +0 -50
  140. package/src/getInsertBetweenVals.ts +0 -31
  141. package/src/getLeftAndRightOfSequenceInRangeGivenPosition.ts +0 -40
  142. package/src/getMassOfAaString.ts +0 -29
  143. package/src/getOrfsFromSequence.ts +0 -132
  144. package/src/getOverlapBetweenTwoSequences.ts +0 -30
  145. package/src/getPossiblePartsFromSequenceAndEnzymes.ts +0 -149
  146. package/src/getReverseAminoAcidStringFromSequenceString.ts +0 -22
  147. package/src/getReverseComplementAminoAcidStringFromSequenceString.ts +0 -10
  148. package/src/getReverseComplementAnnotation.ts +0 -33
  149. package/src/getReverseComplementSequenceAndAnnotations.ts +0 -46
  150. package/src/getReverseComplementSequenceString.ts +0 -18
  151. package/src/getReverseSequenceString.ts +0 -12
  152. package/src/getSequenceDataBetweenRange.ts +0 -154
  153. package/src/getVirtualDigest.ts +0 -139
  154. package/src/guessIfSequenceIsDnaAndNotProtein.ts +0 -39
  155. package/src/index.test.ts +0 -43
  156. package/src/index.ts +0 -111
  157. package/src/insertGapsIntoRefSeq.ts +0 -43
  158. package/src/insertSequenceDataAtPosition.ts +0 -2
  159. package/src/insertSequenceDataAtPositionOrRange.ts +0 -328
  160. package/src/isEnzymeType2S.ts +0 -5
  161. package/src/mapAnnotationsToRows.ts +0 -256
  162. package/src/prepareCircularViewData.ts +0 -24
  163. package/src/prepareRowData.ts +0 -61
  164. package/src/proteinAlphabet.ts +0 -271
  165. package/src/rotateBpsToPosition.ts +0 -12
  166. package/src/rotateSequenceDataToPosition.ts +0 -54
  167. package/src/shiftAnnotationsByLen.ts +0 -24
  168. package/src/threeLetterSequenceStringToAminoAcidMap.ts +0 -198
  169. package/src/tidyUpAnnotation.ts +0 -205
  170. package/src/tidyUpSequenceData.ts +0 -213
  171. package/src/types.ts +0 -109
  172. package/types.d.ts +0 -105
package/index.d.ts CHANGED
@@ -1,14 +1,8 @@
1
+ import { getFeatureToColorMap, getFeatureTypes, genbankFeatureTypes, getMergedFeatureMap } from './featureTypesAndColors';
1
2
  import { autoAnnotate, convertApELikeRegexToRegex, convertProteinSeqToDNAIupac } from './autoAnnotate';
2
- import { genbankFeatureTypes, getFeatureToColorMap, getFeatureTypes, getMergedFeatureMap } from './featureTypesAndColors';
3
3
  export * from './computeDigestFragments';
4
4
  export * from './diffUtils';
5
5
  export * from './annotationTypes';
6
- declare const FeatureTypes: string[];
7
- declare const featureColors: Record<string, string>;
8
- export { getFeatureToColorMap, getFeatureTypes, genbankFeatureTypes, getMergedFeatureMap, FeatureTypes, featureColors };
9
- export { autoAnnotate };
10
- export { convertApELikeRegexToRegex };
11
- export { convertProteinSeqToDNAIupac };
12
6
  export * as bioData from './bioData';
13
7
  export { default as getAllInsertionsInSeqReads } from './getAllInsertionsInSeqReads';
14
8
  export { default as annotateSingleSeq } from './annotateSingleSeq';
@@ -29,7 +23,6 @@ export { default as aliasedEnzymesByName } from './aliasedEnzymesByName';
29
23
  export { default as defaultEnzymesByName } from './defaultEnzymesByName';
30
24
  export { default as generateSequenceData } from './generateSequenceData';
31
25
  export { default as generateAnnotations } from './generateAnnotations';
32
- export { default as filterSequenceString, filterRnaString } from './filterSequenceString';
33
26
  export { default as findNearestRangeOfSequenceOverlapToPosition } from './findNearestRangeOfSequenceOverlapToPosition';
34
27
  export { default as findOrfsInPlasmid } from './findOrfsInPlasmid';
35
28
  export { default as findSequenceMatches } from './findSequenceMatches';
@@ -83,3 +76,7 @@ export { default as degenerateRnaToAminoAcidMap } from './degenerateRnaToAminoAc
83
76
  export { default as getMassOfAaString } from './getMassOfAaString';
84
77
  export { default as shiftAnnotationsByLen } from './shiftAnnotationsByLen';
85
78
  export { default as adjustAnnotationsToInsert } from './adjustAnnotationsToInsert';
79
+ export const FeatureTypes: any[];
80
+ export const featureColors: {};
81
+ export { getFeatureToColorMap, getFeatureTypes, genbankFeatureTypes, getMergedFeatureMap, autoAnnotate, convertApELikeRegexToRegex, convertProteinSeqToDNAIupac };
82
+ export { default as filterSequenceString, filterRnaString } from './filterSequenceString';