@teselagen/sequence-utils 0.3.38-beta.3 → 0.3.41

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (169) hide show
  1. package/DNAComplementMap.d.ts +1 -1
  2. package/addGapsToSeqReads.d.ts +3 -16
  3. package/adjustAnnotationsToInsert.d.ts +1 -2
  4. package/adjustBpsToReplaceOrInsert.d.ts +1 -2
  5. package/aliasedEnzymesByName.d.ts +1 -37
  6. package/aminoAcidToDegenerateDnaMap.d.ts +31 -1
  7. package/aminoAcidToDegenerateRnaMap.d.ts +1 -1
  8. package/annotateSingleSeq.d.ts +4 -5
  9. package/annotationTypes.d.ts +2 -2
  10. package/autoAnnotate.d.ts +8 -17
  11. package/bioData.d.ts +58 -10
  12. package/calculateEndStability.d.ts +1 -1
  13. package/calculateNebTa.d.ts +1 -6
  14. package/calculateNebTm.d.ts +4 -6
  15. package/calculatePercentGC.d.ts +1 -1
  16. package/calculateSantaLuciaTm.d.ts +114 -28
  17. package/calculateTm.d.ts +1 -13
  18. package/computeDigestFragments.d.ts +24 -30
  19. package/condensePairwiseAlignmentDifferences.d.ts +1 -1
  20. package/convertAACaretPositionOrRangeToDna.d.ts +1 -2
  21. package/convertDnaCaretPositionOrRangeToAA.d.ts +1 -2
  22. package/cutSequenceByRestrictionEnzyme.d.ts +1 -2
  23. package/defaultEnzymesByName.d.ts +1 -2
  24. package/degenerateDnaToAminoAcidMap.d.ts +1 -1
  25. package/degenerateRnaToAminoAcidMap.d.ts +1 -1
  26. package/deleteSequenceDataAtRange.d.ts +1 -2
  27. package/diffUtils.d.ts +7 -9
  28. package/doesEnzymeChopOutsideOfRecognitionSite.d.ts +1 -2
  29. package/featureTypesAndColors.d.ts +6 -19
  30. package/filterSequenceString.d.ts +10 -14
  31. package/findApproxMatches.d.ts +1 -7
  32. package/findNearestRangeOfSequenceOverlapToPosition.d.ts +1 -2
  33. package/findOrfsInPlasmid.d.ts +11 -2
  34. package/findSequenceMatches.d.ts +1 -11
  35. package/generateAnnotations.d.ts +1 -2
  36. package/generateSequenceData.d.ts +13 -8
  37. package/getAllInsertionsInSeqReads.d.ts +1 -11
  38. package/getAminoAcidDataForEachBaseOfDna.d.ts +5 -6
  39. package/getAminoAcidFromSequenceTriplet.d.ts +1 -1
  40. package/getAminoAcidStringFromSequenceString.d.ts +1 -3
  41. package/getCodonRangeForAASliver.d.ts +4 -3
  42. package/getComplementAminoAcidStringFromSequenceString.d.ts +1 -1
  43. package/getComplementSequenceAndAnnotations.d.ts +1 -5
  44. package/getComplementSequenceString.d.ts +1 -1
  45. package/getCutsiteType.d.ts +1 -2
  46. package/getCutsitesFromSequence.d.ts +1 -2
  47. package/getDegenerateDnaStringFromAAString.d.ts +1 -1
  48. package/getDegenerateRnaStringFromAAString.d.ts +1 -1
  49. package/getDigestFragmentsForCutsites.d.ts +1 -4
  50. package/getDigestFragmentsForRestrictionEnzymes.d.ts +1 -8
  51. package/getInsertBetweenVals.d.ts +1 -2
  52. package/getLeftAndRightOfSequenceInRangeGivenPosition.d.ts +1 -2
  53. package/getOrfsFromSequence.d.ts +11 -17
  54. package/getOverlapBetweenTwoSequences.d.ts +1 -2
  55. package/getPossiblePartsFromSequenceAndEnzymes.d.ts +1 -18
  56. package/getReverseAminoAcidStringFromSequenceString.d.ts +1 -1
  57. package/getReverseComplementAminoAcidStringFromSequenceString.d.ts +1 -1
  58. package/getReverseComplementAnnotation.d.ts +1 -11
  59. package/getReverseComplementSequenceAndAnnotations.d.ts +1 -5
  60. package/getReverseComplementSequenceString.d.ts +1 -1
  61. package/getReverseSequenceString.d.ts +1 -1
  62. package/getSequenceDataBetweenRange.d.ts +1 -9
  63. package/getVirtualDigest.d.ts +10 -11
  64. package/guessIfSequenceIsDnaAndNotProtein.d.ts +1 -5
  65. package/index.cjs +491 -728
  66. package/index.d.ts +5 -8
  67. package/index.js +491 -728
  68. package/index.umd.cjs +491 -728
  69. package/insertGapsIntoRefSeq.d.ts +1 -2
  70. package/insertSequenceDataAtPositionOrRange.d.ts +1 -10
  71. package/isEnzymeType2S.d.ts +1 -2
  72. package/mapAnnotationsToRows.d.ts +1 -9
  73. package/package.json +9 -12
  74. package/prepareCircularViewData.d.ts +1 -2
  75. package/prepareRowData.d.ts +3 -7
  76. package/proteinAlphabet.d.ts +1 -1
  77. package/rotateBpsToPosition.d.ts +1 -1
  78. package/rotateSequenceDataToPosition.d.ts +1 -3
  79. package/shiftAnnotationsByLen.d.ts +3 -4
  80. package/src/autoAnnotate.test.js +1 -0
  81. package/src/getSequenceDataBetweenRange.js +11 -2
  82. package/src/getSequenceDataBetweenRange.test.js +42 -0
  83. package/src/prepareRowData_output1.json +0 -1
  84. package/threeLetterSequenceStringToAminoAcidMap.d.ts +921 -11
  85. package/tidyUpAnnotation.d.ts +11 -13
  86. package/tidyUpSequenceData.d.ts +1 -15
  87. package/src/DNAComplementMap.ts +0 -32
  88. package/src/addGapsToSeqReads.ts +0 -436
  89. package/src/adjustAnnotationsToInsert.ts +0 -20
  90. package/src/adjustBpsToReplaceOrInsert.ts +0 -73
  91. package/src/aliasedEnzymesByName.ts +0 -7366
  92. package/src/aminoAcidToDegenerateDnaMap.ts +0 -32
  93. package/src/aminoAcidToDegenerateRnaMap.ts +0 -32
  94. package/src/annotateSingleSeq.ts +0 -37
  95. package/src/annotationTypes.ts +0 -23
  96. package/src/autoAnnotate.ts +0 -290
  97. package/src/bioData.ts +0 -65
  98. package/src/calculateEndStability.ts +0 -91
  99. package/src/calculateNebTa.ts +0 -46
  100. package/src/calculateNebTm.ts +0 -132
  101. package/src/calculatePercentGC.ts +0 -3
  102. package/src/calculateSantaLuciaTm.ts +0 -184
  103. package/src/calculateTm.ts +0 -242
  104. package/src/computeDigestFragments.ts +0 -238
  105. package/src/condensePairwiseAlignmentDifferences.ts +0 -85
  106. package/src/convertAACaretPositionOrRangeToDna.ts +0 -28
  107. package/src/convertDnaCaretPositionOrRangeToAA.ts +0 -28
  108. package/src/cutSequenceByRestrictionEnzyme.ts +0 -345
  109. package/src/defaultEnzymesByName.ts +0 -280
  110. package/src/degenerateDnaToAminoAcidMap.ts +0 -5
  111. package/src/degenerateRnaToAminoAcidMap.ts +0 -5
  112. package/src/deleteSequenceDataAtRange.ts +0 -13
  113. package/src/diffUtils.ts +0 -80
  114. package/src/doesEnzymeChopOutsideOfRecognitionSite.ts +0 -16
  115. package/src/featureTypesAndColors.ts +0 -167
  116. package/src/filterSequenceString.ts +0 -153
  117. package/src/findApproxMatches.ts +0 -58
  118. package/src/findNearestRangeOfSequenceOverlapToPosition.ts +0 -43
  119. package/src/findOrfsInPlasmid.ts +0 -31
  120. package/src/findSequenceMatches.ts +0 -154
  121. package/src/generateAnnotations.ts +0 -39
  122. package/src/generateSequenceData.ts +0 -212
  123. package/src/getAllInsertionsInSeqReads.ts +0 -100
  124. package/src/getAminoAcidDataForEachBaseOfDna.ts +0 -305
  125. package/src/getAminoAcidFromSequenceTriplet.ts +0 -27
  126. package/src/getAminoAcidStringFromSequenceString.ts +0 -36
  127. package/src/getCodonRangeForAASliver.ts +0 -73
  128. package/src/getComplementAminoAcidStringFromSequenceString.ts +0 -10
  129. package/src/getComplementSequenceAndAnnotations.ts +0 -25
  130. package/src/getComplementSequenceString.ts +0 -23
  131. package/src/getCutsiteType.ts +0 -18
  132. package/src/getCutsitesFromSequence.ts +0 -22
  133. package/src/getDegenerateDnaStringFromAAString.ts +0 -15
  134. package/src/getDegenerateRnaStringFromAAString.ts +0 -15
  135. package/src/getDigestFragmentsForCutsites.ts +0 -126
  136. package/src/getDigestFragmentsForRestrictionEnzymes.ts +0 -50
  137. package/src/getInsertBetweenVals.ts +0 -31
  138. package/src/getLeftAndRightOfSequenceInRangeGivenPosition.ts +0 -40
  139. package/src/getMassOfAaString.ts +0 -29
  140. package/src/getOrfsFromSequence.ts +0 -132
  141. package/src/getOverlapBetweenTwoSequences.ts +0 -30
  142. package/src/getPossiblePartsFromSequenceAndEnzymes.ts +0 -149
  143. package/src/getReverseAminoAcidStringFromSequenceString.ts +0 -22
  144. package/src/getReverseComplementAminoAcidStringFromSequenceString.ts +0 -10
  145. package/src/getReverseComplementAnnotation.ts +0 -33
  146. package/src/getReverseComplementSequenceAndAnnotations.ts +0 -46
  147. package/src/getReverseComplementSequenceString.ts +0 -18
  148. package/src/getReverseSequenceString.ts +0 -12
  149. package/src/getSequenceDataBetweenRange.ts +0 -154
  150. package/src/getVirtualDigest.ts +0 -139
  151. package/src/guessIfSequenceIsDnaAndNotProtein.ts +0 -39
  152. package/src/index.test.ts +0 -43
  153. package/src/index.ts +0 -111
  154. package/src/insertGapsIntoRefSeq.ts +0 -43
  155. package/src/insertSequenceDataAtPosition.ts +0 -2
  156. package/src/insertSequenceDataAtPositionOrRange.ts +0 -328
  157. package/src/isEnzymeType2S.ts +0 -5
  158. package/src/mapAnnotationsToRows.ts +0 -256
  159. package/src/prepareCircularViewData.ts +0 -24
  160. package/src/prepareRowData.ts +0 -61
  161. package/src/proteinAlphabet.ts +0 -271
  162. package/src/rotateBpsToPosition.ts +0 -12
  163. package/src/rotateSequenceDataToPosition.ts +0 -54
  164. package/src/shiftAnnotationsByLen.ts +0 -24
  165. package/src/threeLetterSequenceStringToAminoAcidMap.ts +0 -198
  166. package/src/tidyUpAnnotation.ts +0 -205
  167. package/src/tidyUpSequenceData.ts +0 -213
  168. package/src/types.ts +0 -109
  169. package/types.d.ts +0 -105

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