@teselagen/sequence-utils 0.3.37 → 0.3.38-beta.2

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 (168) hide show
  1. package/DNAComplementMap.d.ts +1 -1
  2. package/addGapsToSeqReads.d.ts +16 -3
  3. package/adjustAnnotationsToInsert.d.ts +2 -1
  4. package/adjustBpsToReplaceOrInsert.d.ts +2 -1
  5. package/aliasedEnzymesByName.d.ts +37 -1
  6. package/aminoAcidToDegenerateDnaMap.d.ts +1 -31
  7. package/aminoAcidToDegenerateRnaMap.d.ts +1 -1
  8. package/annotateSingleSeq.d.ts +5 -4
  9. package/annotationTypes.d.ts +2 -2
  10. package/autoAnnotate.d.ts +17 -8
  11. package/bioData.d.ts +10 -58
  12. package/calculateEndStability.d.ts +1 -1
  13. package/calculateNebTa.d.ts +6 -1
  14. package/calculateNebTm.d.ts +6 -4
  15. package/calculatePercentGC.d.ts +1 -1
  16. package/calculateSantaLuciaTm.d.ts +28 -114
  17. package/calculateTm.d.ts +13 -1
  18. package/computeDigestFragments.d.ts +30 -24
  19. package/condensePairwiseAlignmentDifferences.d.ts +1 -1
  20. package/convertAACaretPositionOrRangeToDna.d.ts +2 -1
  21. package/convertDnaCaretPositionOrRangeToAA.d.ts +2 -1
  22. package/cutSequenceByRestrictionEnzyme.d.ts +2 -1
  23. package/defaultEnzymesByName.d.ts +2 -1
  24. package/degenerateDnaToAminoAcidMap.d.ts +1 -1
  25. package/degenerateRnaToAminoAcidMap.d.ts +1 -1
  26. package/deleteSequenceDataAtRange.d.ts +2 -1
  27. package/diffUtils.d.ts +9 -7
  28. package/doesEnzymeChopOutsideOfRecognitionSite.d.ts +2 -1
  29. package/featureTypesAndColors.d.ts +19 -6
  30. package/filterSequenceString.d.ts +14 -10
  31. package/findApproxMatches.d.ts +7 -1
  32. package/findNearestRangeOfSequenceOverlapToPosition.d.ts +2 -1
  33. package/findOrfsInPlasmid.d.ts +2 -11
  34. package/findSequenceMatches.d.ts +11 -1
  35. package/generateAnnotations.d.ts +2 -1
  36. package/generateSequenceData.d.ts +8 -13
  37. package/getAllInsertionsInSeqReads.d.ts +11 -1
  38. package/getAminoAcidDataForEachBaseOfDna.d.ts +6 -5
  39. package/getAminoAcidFromSequenceTriplet.d.ts +1 -1
  40. package/getAminoAcidStringFromSequenceString.d.ts +3 -1
  41. package/getCodonRangeForAASliver.d.ts +3 -4
  42. package/getComplementAminoAcidStringFromSequenceString.d.ts +1 -1
  43. package/getComplementSequenceAndAnnotations.d.ts +5 -1
  44. package/getComplementSequenceString.d.ts +1 -1
  45. package/getCutsiteType.d.ts +2 -1
  46. package/getCutsitesFromSequence.d.ts +2 -1
  47. package/getDegenerateDnaStringFromAAString.d.ts +1 -1
  48. package/getDegenerateRnaStringFromAAString.d.ts +1 -1
  49. package/getDigestFragmentsForCutsites.d.ts +4 -1
  50. package/getDigestFragmentsForRestrictionEnzymes.d.ts +8 -1
  51. package/getInsertBetweenVals.d.ts +2 -1
  52. package/getLeftAndRightOfSequenceInRangeGivenPosition.d.ts +2 -1
  53. package/getOrfsFromSequence.d.ts +17 -11
  54. package/getOverlapBetweenTwoSequences.d.ts +2 -1
  55. package/getPossiblePartsFromSequenceAndEnzymes.d.ts +18 -1
  56. package/getReverseAminoAcidStringFromSequenceString.d.ts +1 -1
  57. package/getReverseComplementAminoAcidStringFromSequenceString.d.ts +1 -1
  58. package/getReverseComplementAnnotation.d.ts +11 -1
  59. package/getReverseComplementSequenceAndAnnotations.d.ts +5 -1
  60. package/getReverseComplementSequenceString.d.ts +1 -1
  61. package/getReverseSequenceString.d.ts +1 -1
  62. package/getSequenceDataBetweenRange.d.ts +9 -1
  63. package/getVirtualDigest.d.ts +11 -10
  64. package/guessIfSequenceIsDnaAndNotProtein.d.ts +5 -1
  65. package/index.cjs +732 -483
  66. package/index.d.ts +8 -5
  67. package/index.js +732 -483
  68. package/index.umd.cjs +732 -483
  69. package/insertGapsIntoRefSeq.d.ts +2 -1
  70. package/insertSequenceDataAtPositionOrRange.d.ts +10 -1
  71. package/isEnzymeType2S.d.ts +2 -1
  72. package/mapAnnotationsToRows.d.ts +9 -1
  73. package/package.json +9 -6
  74. package/prepareCircularViewData.d.ts +2 -1
  75. package/prepareRowData.d.ts +7 -3
  76. package/proteinAlphabet.d.ts +1 -1
  77. package/rotateBpsToPosition.d.ts +1 -1
  78. package/rotateSequenceDataToPosition.d.ts +3 -1
  79. package/shiftAnnotationsByLen.d.ts +4 -3
  80. package/src/DNAComplementMap.ts +32 -0
  81. package/src/addGapsToSeqReads.ts +436 -0
  82. package/src/adjustAnnotationsToInsert.ts +20 -0
  83. package/src/adjustBpsToReplaceOrInsert.ts +73 -0
  84. package/src/aliasedEnzymesByName.ts +7366 -0
  85. package/src/aminoAcidToDegenerateDnaMap.ts +32 -0
  86. package/src/aminoAcidToDegenerateRnaMap.ts +32 -0
  87. package/src/annotateSingleSeq.ts +37 -0
  88. package/src/annotationTypes.ts +23 -0
  89. package/src/autoAnnotate.test.js +0 -1
  90. package/src/autoAnnotate.ts +290 -0
  91. package/src/bioData.ts +65 -0
  92. package/src/calculateEndStability.ts +91 -0
  93. package/src/calculateNebTa.ts +46 -0
  94. package/src/calculateNebTm.ts +132 -0
  95. package/src/calculatePercentGC.ts +3 -0
  96. package/src/calculateSantaLuciaTm.ts +184 -0
  97. package/src/calculateTm.ts +242 -0
  98. package/src/computeDigestFragments.ts +238 -0
  99. package/src/condensePairwiseAlignmentDifferences.ts +85 -0
  100. package/src/convertAACaretPositionOrRangeToDna.ts +28 -0
  101. package/src/convertDnaCaretPositionOrRangeToAA.ts +28 -0
  102. package/src/cutSequenceByRestrictionEnzyme.ts +345 -0
  103. package/src/defaultEnzymesByName.ts +280 -0
  104. package/src/degenerateDnaToAminoAcidMap.ts +5 -0
  105. package/src/degenerateRnaToAminoAcidMap.ts +5 -0
  106. package/src/deleteSequenceDataAtRange.ts +13 -0
  107. package/src/diffUtils.ts +80 -0
  108. package/src/doesEnzymeChopOutsideOfRecognitionSite.ts +16 -0
  109. package/src/featureTypesAndColors.ts +167 -0
  110. package/src/filterSequenceString.ts +153 -0
  111. package/src/findApproxMatches.ts +58 -0
  112. package/src/findNearestRangeOfSequenceOverlapToPosition.ts +43 -0
  113. package/src/findOrfsInPlasmid.js +6 -1
  114. package/src/findOrfsInPlasmid.ts +31 -0
  115. package/src/findSequenceMatches.ts +154 -0
  116. package/src/generateAnnotations.ts +39 -0
  117. package/src/generateSequenceData.ts +212 -0
  118. package/src/getAllInsertionsInSeqReads.ts +100 -0
  119. package/src/getAminoAcidDataForEachBaseOfDna.ts +305 -0
  120. package/src/getAminoAcidFromSequenceTriplet.ts +27 -0
  121. package/src/getAminoAcidStringFromSequenceString.ts +36 -0
  122. package/src/getCodonRangeForAASliver.ts +73 -0
  123. package/src/getComplementAminoAcidStringFromSequenceString.ts +10 -0
  124. package/src/getComplementSequenceAndAnnotations.ts +25 -0
  125. package/src/getComplementSequenceString.ts +23 -0
  126. package/src/getCutsiteType.ts +18 -0
  127. package/src/getCutsitesFromSequence.ts +22 -0
  128. package/src/getDegenerateDnaStringFromAAString.ts +15 -0
  129. package/src/getDegenerateRnaStringFromAAString.ts +15 -0
  130. package/src/getDigestFragmentsForCutsites.ts +126 -0
  131. package/src/getDigestFragmentsForRestrictionEnzymes.ts +50 -0
  132. package/src/getInsertBetweenVals.ts +31 -0
  133. package/src/getLeftAndRightOfSequenceInRangeGivenPosition.ts +40 -0
  134. package/src/getMassOfAaString.ts +29 -0
  135. package/src/getOrfsFromSequence.ts +132 -0
  136. package/src/getOverlapBetweenTwoSequences.ts +30 -0
  137. package/src/getPossiblePartsFromSequenceAndEnzymes.ts +149 -0
  138. package/src/getReverseAminoAcidStringFromSequenceString.ts +22 -0
  139. package/src/getReverseComplementAminoAcidStringFromSequenceString.ts +10 -0
  140. package/src/getReverseComplementAnnotation.ts +33 -0
  141. package/src/getReverseComplementSequenceAndAnnotations.ts +46 -0
  142. package/src/getReverseComplementSequenceString.ts +18 -0
  143. package/src/getReverseSequenceString.ts +12 -0
  144. package/src/getSequenceDataBetweenRange.ts +154 -0
  145. package/src/getVirtualDigest.ts +139 -0
  146. package/src/guessIfSequenceIsDnaAndNotProtein.ts +39 -0
  147. package/src/index.test.ts +43 -0
  148. package/src/index.ts +111 -0
  149. package/src/insertGapsIntoRefSeq.ts +43 -0
  150. package/src/insertSequenceDataAtPosition.ts +2 -0
  151. package/src/insertSequenceDataAtPositionOrRange.ts +328 -0
  152. package/src/isEnzymeType2S.ts +5 -0
  153. package/src/mapAnnotationsToRows.ts +256 -0
  154. package/src/prepareCircularViewData.ts +24 -0
  155. package/src/prepareRowData.ts +61 -0
  156. package/src/prepareRowData_output1.json +1 -0
  157. package/src/proteinAlphabet.ts +271 -0
  158. package/src/rotateBpsToPosition.ts +12 -0
  159. package/src/rotateSequenceDataToPosition.ts +54 -0
  160. package/src/shiftAnnotationsByLen.ts +24 -0
  161. package/src/threeLetterSequenceStringToAminoAcidMap.ts +198 -0
  162. package/src/tidyUpAnnotation.ts +205 -0
  163. package/src/tidyUpSequenceData.ts +213 -0
  164. package/src/types.ts +109 -0
  165. package/threeLetterSequenceStringToAminoAcidMap.d.ts +11 -921
  166. package/tidyUpAnnotation.d.ts +13 -11
  167. package/tidyUpSequenceData.d.ts +15 -1
  168. package/types.d.ts +105 -0

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