@teselagen/sequence-utils 0.1.21 → 0.1.23

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Files changed (135) hide show
  1. package/index.js +12030 -26126
  2. package/index.mjs +12119 -26124
  3. package/index.umd.js +24056 -38154
  4. package/package.json +2 -2
  5. package/src/DNAComplementMap.js +32 -0
  6. package/src/addGapsToSeqReads.js +417 -0
  7. package/src/addGapsToSeqReads.test.js +358 -0
  8. package/src/adjustAnnotationsToInsert.js +19 -0
  9. package/src/adjustBpsToReplaceOrInsert.js +50 -0
  10. package/src/adjustBpsToReplaceOrInsert.test.js +59 -0
  11. package/src/aliasedEnzymesByName.js +7363 -0
  12. package/src/aminoAcidToDegenerateDnaMap.js +32 -0
  13. package/src/aminoAcidToDegenerateRnaMap.js +32 -0
  14. package/src/aminoAcidToDnaRna.test.js +27 -0
  15. package/src/annotateSingleSeq.js +29 -0
  16. package/src/annotateSingleSeq.test.js +64 -0
  17. package/src/annotationTypes.js +23 -0
  18. package/src/autoAnnotate.js +242 -0
  19. package/src/autoAnnotate.test.js +1039 -0
  20. package/src/bioData.js +431 -0
  21. package/src/calculateNebTa.js +34 -0
  22. package/src/calculateNebTa.test.js +57 -0
  23. package/src/calculateNebTm.js +127 -0
  24. package/src/calculateNebTm.test.js +32 -0
  25. package/src/calculatePercentGC.js +3 -0
  26. package/src/calculatePercentGC.test.js +14 -0
  27. package/src/calculateTm.js +297 -0
  28. package/src/calculateTm.test.js +7 -0
  29. package/src/computeDigestFragments.js +179 -0
  30. package/src/computeDigestFragments.test.js +73 -0
  31. package/src/condensePairwiseAlignmentDifferences.js +85 -0
  32. package/src/condensePairwiseAlignmentDifferences.test.js +66 -0
  33. package/src/convertAACaretPositionOrRangeToDna.js +24 -0
  34. package/src/convertAACaretPositionOrRangeToDna.test.js +34 -0
  35. package/src/convertDnaCaretPositionOrRangeToAA.js +24 -0
  36. package/src/convertDnaCaretPositionOrRangeToAA.test.js +37 -0
  37. package/src/cutSequenceByRestrictionEnzyme.js +301 -0
  38. package/src/cutSequenceByRestrictionEnzyme.test.js +296 -0
  39. package/src/defaultEnzymesByName.js +278 -0
  40. package/src/degenerateDnaToAminoAcidMap.js +5 -0
  41. package/src/degenerateRnaToAminoAcidMap.js +5 -0
  42. package/src/deleteSequenceDataAtRange.js +5 -0
  43. package/src/deleteSequenceDataAtRange.test.js +146 -0
  44. package/src/diffUtils.js +64 -0
  45. package/src/diffUtils.test.js +74 -0
  46. package/src/doesEnzymeChopOutsideOfRecognitionSite.js +10 -0
  47. package/src/doesEnzymeChopOutsideOfRecognitionSite.test.js +41 -0
  48. package/src/featureTypesAndColors.js +152 -0
  49. package/src/featureTypesAndColors.test.js +52 -0
  50. package/src/filterAminoAcidSequenceString.js +13 -0
  51. package/src/filterAminoAcidSequenceString.test.js +22 -0
  52. package/src/filterSequenceString.js +22 -0
  53. package/src/filterSequenceString.test.js +13 -0
  54. package/src/findNearestRangeOfSequenceOverlapToPosition.js +39 -0
  55. package/src/findNearestRangeOfSequenceOverlapToPosition.test.js +31 -0
  56. package/src/findOrfsInPlasmid.js +26 -0
  57. package/src/findSequenceMatches.js +133 -0
  58. package/src/findSequenceMatches.test.js +286 -0
  59. package/src/generateAnnotations.js +34 -0
  60. package/src/generateSequenceData.js +206 -0
  61. package/src/generateSequenceData.test.js +22 -0
  62. package/src/getAllInsertionsInSeqReads.js +83 -0
  63. package/src/getAllInsertionsInSeqReads.test.js +26 -0
  64. package/src/getAminoAcidDataForEachBaseOfDna.js +163 -0
  65. package/src/getAminoAcidDataForEachBaseOfDna.test.js +424 -0
  66. package/src/getAminoAcidFromSequenceTriplet.js +22 -0
  67. package/src/getAminoAcidStringFromSequenceString.js +18 -0
  68. package/src/getAminoAcidStringFromSequenceString.test.js +18 -0
  69. package/src/getCodonRangeForAASliver.js +63 -0
  70. package/src/getComplementAminoAcidStringFromSequenceString.js +11 -0
  71. package/src/getComplementSequenceAndAnnotations.js +20 -0
  72. package/src/getComplementSequenceString.js +19 -0
  73. package/src/getComplementSequenceString.test.js +13 -0
  74. package/src/getCutsiteType.js +10 -0
  75. package/src/getCutsitesFromSequence.js +17 -0
  76. package/src/getDegenerateDnaStringFromAAString.js +8 -0
  77. package/src/getDegenerateRnaStringFromAAString.js +8 -0
  78. package/src/getDigestFragmentsForCutsites.js +105 -0
  79. package/src/getDigestFragmentsForRestrictionEnzymes.js +27 -0
  80. package/src/getDigestFragmentsForRestrictionEnzymes.test.js +228 -0
  81. package/src/getInsertBetweenVals.js +28 -0
  82. package/src/getInsertBetweenVals.test.js +33 -0
  83. package/src/getLeftAndRightOfSequenceInRangeGivenPosition.js +39 -0
  84. package/src/getLeftAndRightOfSequenceInRangeGivenPosition.test.js +80 -0
  85. package/src/getMassOfAaString.js +24 -0
  86. package/src/getMassofAaString.test.js +18 -0
  87. package/src/getOrfsFromSequence.js +124 -0
  88. package/src/getOrfsFromSequence.test.js +210 -0
  89. package/src/getOverlapBetweenTwoSequences.js +30 -0
  90. package/src/getOverlapBetweenTwoSequences.test.js +23 -0
  91. package/src/getPossiblePartsFromSequenceAndEnzymes.js +121 -0
  92. package/src/getPossiblePartsFromSequenceAndEnzymes.test.js +208 -0
  93. package/src/getReverseAminoAcidStringFromSequenceString.js +20 -0
  94. package/src/getReverseAminoAcidStringFromSequenceString.test.js +11 -0
  95. package/src/getReverseComplementAminoAcidStringFromSequenceString.js +7 -0
  96. package/src/getReverseComplementAnnotation.js +23 -0
  97. package/src/getReverseComplementAnnotation.test.js +44 -0
  98. package/src/getReverseComplementSequenceAndAnnotations.js +38 -0
  99. package/src/getReverseComplementSequenceAndAnnotations.test.js +105 -0
  100. package/src/getReverseComplementSequenceString.js +17 -0
  101. package/src/getReverseComplementSequenceString.test.js +11 -0
  102. package/src/getReverseSequenceString.js +12 -0
  103. package/src/getReverseSequenceString.test.js +9 -0
  104. package/src/getSequenceDataBetweenRange.js +131 -0
  105. package/src/getSequenceDataBetweenRange.test.js +474 -0
  106. package/src/getVirtualDigest.js +125 -0
  107. package/src/getVirtualDigest.test.js +134 -0
  108. package/src/guessIfSequenceIsDnaAndNotProtein.js +33 -0
  109. package/src/guessIfSequenceIsDnaAndNotProtein.test.js +34 -0
  110. package/src/index.js +106 -0
  111. package/src/index.test.js +38 -0
  112. package/src/insertGapsIntoRefSeq.js +38 -0
  113. package/src/insertGapsIntoRefSeq.test.js +20 -0
  114. package/src/insertSequenceDataAtPosition.js +2 -0
  115. package/src/insertSequenceDataAtPosition.test.js +75 -0
  116. package/src/insertSequenceDataAtPositionOrRange.js +249 -0
  117. package/src/insertSequenceDataAtPositionOrRange.test.js +547 -0
  118. package/src/isEnzymeType2S.js +3 -0
  119. package/src/mapAnnotationsToRows.js +174 -0
  120. package/src/mapAnnotationsToRows.test.js +425 -0
  121. package/src/prepareCircularViewData.js +17 -0
  122. package/src/prepareCircularViewData.test.js +196 -0
  123. package/src/prepareRowData.js +41 -0
  124. package/src/prepareRowData.test.js +36 -0
  125. package/src/prepareRowData_output1.json +391 -0
  126. package/src/proteinAlphabet.js +257 -0
  127. package/src/rotateBpsToPosition.js +13 -0
  128. package/src/rotateBpsToPosition.test.js +6 -0
  129. package/src/rotateSequenceDataToPosition.js +48 -0
  130. package/src/rotateSequenceDataToPosition.test.js +71 -0
  131. package/src/shiftAnnotationsByLen.js +17 -0
  132. package/src/threeLetterSequenceStringToAminoAcidMap.js +106 -0
  133. package/src/tidyUpAnnotation.js +182 -0
  134. package/src/tidyUpSequenceData.js +169 -0
  135. package/src/tidyUpSequenceData.test.js +332 -0

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