@teselagen/sequence-utils 0.3.24 → 0.3.26

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Files changed (45) hide show
  1. package/calculateNebTm.d.ts +3 -2
  2. package/calculateTm.d.ts +7 -1
  3. package/degenerateDnaToAminoAcidMap.d.ts +1 -1
  4. package/degenerateRnaToAminoAcidMap.d.ts +1 -1
  5. package/getAminoAcidDataForEachBaseOfDna.d.ts +13 -3
  6. package/{index.mjs → index.cjs} +2769 -6273
  7. package/index.d.ts +76 -81
  8. package/index.js +2738 -6242
  9. package/{index.umd.js → index.umd.cjs} +2648 -6152
  10. package/insertSequenceDataAtPosition.d.ts +1 -1
  11. package/package.json +1 -1
  12. package/src/addGapsToSeqReads.js +1 -1
  13. package/src/adjustAnnotationsToInsert.js +1 -1
  14. package/src/autoAnnotate.js +1 -1
  15. package/src/calculateNebTm.js +1 -2
  16. package/src/calculateNebTm.test.js +16 -7
  17. package/src/calculateTm.js +54 -17
  18. package/src/calculateTm.test.js +7 -1
  19. package/src/computeDigestFragments.js +1 -1
  20. package/src/cutSequenceByRestrictionEnzyme.js +1 -1
  21. package/src/degenerateDnaToAminoAcidMap.js +1 -1
  22. package/src/degenerateRnaToAminoAcidMap.js +1 -1
  23. package/src/deleteSequenceDataAtRange.test.js +1 -1
  24. package/src/diffUtils.js +1 -1
  25. package/src/diffUtils.test.js +1 -1
  26. package/src/featureTypesAndColors.js +1 -1
  27. package/src/filterSequenceString.js +1 -1
  28. package/src/findSequenceMatches.js +1 -1
  29. package/src/generateSequenceData.test.js +1 -1
  30. package/src/getAminoAcidDataForEachBaseOfDna.js +246 -115
  31. package/src/getAminoAcidDataForEachBaseOfDna.test.js +55 -0
  32. package/src/getComplementSequenceString.js +1 -1
  33. package/src/getDigestFragmentsForRestrictionEnzymes.js +1 -1
  34. package/src/getReverseComplementAnnotation.js +9 -1
  35. package/src/getReverseComplementSequenceAndAnnotations.js +1 -1
  36. package/src/getReverseComplementSequenceAndAnnotations.test.js +51 -0
  37. package/src/getSequenceDataBetweenRange.js +1 -1
  38. package/src/getVirtualDigest.js +1 -1
  39. package/src/insertSequenceDataAtPositionOrRange.js +1 -1
  40. package/src/insertSequenceDataAtPositionOrRange.test.js +22 -0
  41. package/src/mapAnnotationsToRows.js +1 -1
  42. package/src/prepareCircularViewData.js +1 -1
  43. package/src/rotateSequenceDataToPosition.js +1 -1
  44. package/src/tidyUpAnnotation.js +1 -1
  45. package/src/tidyUpSequenceData.js +9 -2
package/index.d.ts CHANGED
@@ -1,84 +1,79 @@
1
- export * from "./computeDigestFragments";
2
- export * from "./diffUtils";
3
- export * from "./annotationTypes";
4
- export * as bioData from "./bioData";
5
- export { default as getAllInsertionsInSeqReads } from "./getAllInsertionsInSeqReads";
6
- export { default as annotateSingleSeq } from "./annotateSingleSeq";
7
- export { default as getDegenerateDnaStringFromAAString } from "./getDegenerateDnaStringFromAAString";
8
- export { default as getDegenerateRnaStringFromAAString } from "./getDegenerateRnaStringFromAAString";
9
- export { default as getVirtualDigest } from "./getVirtualDigest";
10
- export { default as isEnzymeType2S } from "./isEnzymeType2S";
11
- export { default as insertGapsIntoRefSeq } from "./insertGapsIntoRefSeq";
12
- export { default as adjustBpsToReplaceOrInsert } from "./adjustBpsToReplaceOrInsert";
13
- export { default as calculatePercentGC } from "./calculatePercentGC";
14
- export { default as calculateTm } from "./calculateTm";
15
- export { default as cutSequenceByRestrictionEnzyme } from "./cutSequenceByRestrictionEnzyme";
16
- export { default as deleteSequenceDataAtRange } from "./deleteSequenceDataAtRange";
17
- export { default as DNAComplementMap } from "./DNAComplementMap";
18
- export { default as doesEnzymeChopOutsideOfRecognitionSite } from "./doesEnzymeChopOutsideOfRecognitionSite";
19
- export { default as aliasedEnzymesByName } from "./aliasedEnzymesByName";
20
- export { default as defaultEnzymesByName } from "./defaultEnzymesByName";
21
- export { default as generateSequenceData } from "./generateSequenceData";
22
- export { default as generateAnnotations } from "./generateAnnotations";
23
- export { default as findNearestRangeOfSequenceOverlapToPosition } from "./findNearestRangeOfSequenceOverlapToPosition";
24
- export { default as findOrfsInPlasmid } from "./findOrfsInPlasmid";
25
- export { default as findSequenceMatches } from "./findSequenceMatches";
26
- export { default as getAminoAcidDataForEachBaseOfDna } from "./getAminoAcidDataForEachBaseOfDna";
27
- export { default as getAminoAcidFromSequenceTriplet } from "./getAminoAcidFromSequenceTriplet";
28
- export { default as getAminoAcidStringFromSequenceString } from "./getAminoAcidStringFromSequenceString";
29
- export { default as getCodonRangeForAASliver } from "./getCodonRangeForAASliver";
30
- export { default as getComplementAminoAcidStringFromSequenceString } from "./getComplementAminoAcidStringFromSequenceString";
31
- export { default as getComplementSequenceAndAnnotations } from "./getComplementSequenceAndAnnotations";
32
- export { default as getComplementSequenceString } from "./getComplementSequenceString";
33
- export { default as getCutsitesFromSequence } from "./getCutsitesFromSequence";
34
- export { default as getCutsiteType } from "./getCutsiteType";
35
- export { default as getInsertBetweenVals } from "./getInsertBetweenVals";
36
- export { default as getLeftAndRightOfSequenceInRangeGivenPosition } from "./getLeftAndRightOfSequenceInRangeGivenPosition";
37
- export { default as getOrfsFromSequence } from "./getOrfsFromSequence";
38
- export { default as getOverlapBetweenTwoSequences } from "./getOverlapBetweenTwoSequences";
39
- export { default as getPossiblePartsFromSequenceAndEnzymes } from "./getPossiblePartsFromSequenceAndEnzymes";
40
- export { default as getReverseAminoAcidStringFromSequenceString } from "./getReverseAminoAcidStringFromSequenceString";
41
- export { default as getReverseComplementAminoAcidStringFromSequenceString } from "./getReverseComplementAminoAcidStringFromSequenceString";
42
- export { default as getReverseComplementAnnotation } from "./getReverseComplementAnnotation";
43
- export { default as getReverseComplementSequenceAndAnnotations } from "./getReverseComplementSequenceAndAnnotations";
44
- export { default as getReverseComplementSequenceString } from "./getReverseComplementSequenceString";
45
- export { default as getReverseSequenceString } from "./getReverseSequenceString";
46
- export { default as getSequenceDataBetweenRange } from "./getSequenceDataBetweenRange";
47
- export { default as guessIfSequenceIsDnaAndNotProtein } from "./guessIfSequenceIsDnaAndNotProtein";
48
- export { default as insertSequenceDataAtPosition } from "./insertSequenceDataAtPosition";
49
- export { default as insertSequenceDataAtPositionOrRange } from "./insertSequenceDataAtPositionOrRange";
50
- export { default as mapAnnotationsToRows } from "./mapAnnotationsToRows";
51
- export { default as prepareCircularViewData } from "./prepareCircularViewData";
52
- export { default as prepareRowData } from "./prepareRowData";
53
- export { default as proteinAlphabet } from "./proteinAlphabet";
54
- export { default as rotateSequenceDataToPosition } from "./rotateSequenceDataToPosition";
55
- export { default as rotateBpsToPosition } from "./rotateBpsToPosition";
56
- export { default as threeLetterSequenceStringToAminoAcidMap } from "./threeLetterSequenceStringToAminoAcidMap";
57
- export { default as tidyUpSequenceData } from "./tidyUpSequenceData";
58
- export { default as tidyUpAnnotation } from "./tidyUpAnnotation";
59
- export { default as condensePairwiseAlignmentDifferences } from "./condensePairwiseAlignmentDifferences";
60
- export { default as addGapsToSeqReads } from "./addGapsToSeqReads";
61
- export { default as calculateNebTm } from "./calculateNebTm";
62
- export { default as calculateNebTa } from "./calculateNebTa";
63
- export { default as getDigestFragmentsForCutsites } from "./getDigestFragmentsForCutsites";
64
- export { default as getDigestFragmentsForRestrictionEnzymes } from "./getDigestFragmentsForRestrictionEnzymes";
65
- export { default as convertDnaCaretPositionOrRangeToAA } from "./convertDnaCaretPositionOrRangeToAA";
66
- export { default as convertAACaretPositionOrRangeToDna } from "./convertAACaretPositionOrRangeToDna";
67
- export { default as aminoAcidToDegenerateDnaMap } from "./aminoAcidToDegenerateDnaMap";
68
- export { default as aminoAcidToDegenerateRnaMap } from "./aminoAcidToDegenerateRnaMap";
69
- export { default as degenerateDnaToAminoAcidMap } from "./degenerateDnaToAminoAcidMap";
70
- export { default as degenerateRnaToAminoAcidMap } from "./degenerateRnaToAminoAcidMap";
71
- export { default as getMassOfAaString } from "./getMassOfAaString";
72
- export { default as shiftAnnotationsByLen } from "./shiftAnnotationsByLen";
73
- export { default as adjustAnnotationsToInsert } from "./adjustAnnotationsToInsert";
74
- import { getFeatureToColorMap } from "./featureTypesAndColors";
75
- import { getFeatureTypes } from "./featureTypesAndColors";
76
- import { genbankFeatureTypes } from "./featureTypesAndColors";
77
- import { getMergedFeatureMap } from "./featureTypesAndColors";
1
+ import { getFeatureToColorMap, getFeatureTypes, genbankFeatureTypes, getMergedFeatureMap } from './featureTypesAndColors';
2
+ import { autoAnnotate, convertApELikeRegexToRegex, convertProteinSeqToDNAIupac } from './autoAnnotate';
3
+ export * from './computeDigestFragments';
4
+ export * from './diffUtils';
5
+ export * from './annotationTypes';
6
+ export * as bioData from './bioData';
7
+ export { default as getAllInsertionsInSeqReads } from './getAllInsertionsInSeqReads';
8
+ export { default as annotateSingleSeq } from './annotateSingleSeq';
9
+ export { default as getDegenerateDnaStringFromAAString } from './getDegenerateDnaStringFromAAString';
10
+ export { default as getDegenerateRnaStringFromAAString } from './getDegenerateRnaStringFromAAString';
11
+ export { default as getVirtualDigest } from './getVirtualDigest';
12
+ export { default as isEnzymeType2S } from './isEnzymeType2S';
13
+ export { default as insertGapsIntoRefSeq } from './insertGapsIntoRefSeq';
14
+ export { default as adjustBpsToReplaceOrInsert } from './adjustBpsToReplaceOrInsert';
15
+ export { default as calculatePercentGC } from './calculatePercentGC';
16
+ export { default as calculateTm } from './calculateTm';
17
+ export { default as cutSequenceByRestrictionEnzyme } from './cutSequenceByRestrictionEnzyme';
18
+ export { default as deleteSequenceDataAtRange } from './deleteSequenceDataAtRange';
19
+ export { default as DNAComplementMap } from './DNAComplementMap';
20
+ export { default as doesEnzymeChopOutsideOfRecognitionSite } from './doesEnzymeChopOutsideOfRecognitionSite';
21
+ export { default as aliasedEnzymesByName } from './aliasedEnzymesByName';
22
+ export { default as defaultEnzymesByName } from './defaultEnzymesByName';
23
+ export { default as generateSequenceData } from './generateSequenceData';
24
+ export { default as generateAnnotations } from './generateAnnotations';
25
+ export { default as findNearestRangeOfSequenceOverlapToPosition } from './findNearestRangeOfSequenceOverlapToPosition';
26
+ export { default as findOrfsInPlasmid } from './findOrfsInPlasmid';
27
+ export { default as findSequenceMatches } from './findSequenceMatches';
28
+ export { default as getAminoAcidDataForEachBaseOfDna } from './getAminoAcidDataForEachBaseOfDna';
29
+ export { default as getAminoAcidFromSequenceTriplet } from './getAminoAcidFromSequenceTriplet';
30
+ export { default as getAminoAcidStringFromSequenceString } from './getAminoAcidStringFromSequenceString';
31
+ export { default as getCodonRangeForAASliver } from './getCodonRangeForAASliver';
32
+ export { default as getComplementAminoAcidStringFromSequenceString } from './getComplementAminoAcidStringFromSequenceString';
33
+ export { default as getComplementSequenceAndAnnotations } from './getComplementSequenceAndAnnotations';
34
+ export { default as getComplementSequenceString } from './getComplementSequenceString';
35
+ export { default as getCutsitesFromSequence } from './getCutsitesFromSequence';
36
+ export { default as getCutsiteType } from './getCutsiteType';
37
+ export { default as getInsertBetweenVals } from './getInsertBetweenVals';
38
+ export { default as getLeftAndRightOfSequenceInRangeGivenPosition } from './getLeftAndRightOfSequenceInRangeGivenPosition';
39
+ export { default as getOrfsFromSequence } from './getOrfsFromSequence';
40
+ export { default as getOverlapBetweenTwoSequences } from './getOverlapBetweenTwoSequences';
41
+ export { default as getPossiblePartsFromSequenceAndEnzymes } from './getPossiblePartsFromSequenceAndEnzymes';
42
+ export { default as getReverseAminoAcidStringFromSequenceString } from './getReverseAminoAcidStringFromSequenceString';
43
+ export { default as getReverseComplementAminoAcidStringFromSequenceString } from './getReverseComplementAminoAcidStringFromSequenceString';
44
+ export { default as getReverseComplementAnnotation } from './getReverseComplementAnnotation';
45
+ export { default as getReverseComplementSequenceAndAnnotations } from './getReverseComplementSequenceAndAnnotations';
46
+ export { default as getReverseComplementSequenceString } from './getReverseComplementSequenceString';
47
+ export { default as getReverseSequenceString } from './getReverseSequenceString';
48
+ export { default as getSequenceDataBetweenRange } from './getSequenceDataBetweenRange';
49
+ export { default as guessIfSequenceIsDnaAndNotProtein } from './guessIfSequenceIsDnaAndNotProtein';
50
+ export { default as insertSequenceDataAtPosition } from './insertSequenceDataAtPosition';
51
+ export { default as insertSequenceDataAtPositionOrRange } from './insertSequenceDataAtPositionOrRange';
52
+ export { default as mapAnnotationsToRows } from './mapAnnotationsToRows';
53
+ export { default as prepareCircularViewData } from './prepareCircularViewData';
54
+ export { default as prepareRowData } from './prepareRowData';
55
+ export { default as proteinAlphabet } from './proteinAlphabet';
56
+ export { default as rotateSequenceDataToPosition } from './rotateSequenceDataToPosition';
57
+ export { default as rotateBpsToPosition } from './rotateBpsToPosition';
58
+ export { default as threeLetterSequenceStringToAminoAcidMap } from './threeLetterSequenceStringToAminoAcidMap';
59
+ export { default as tidyUpSequenceData } from './tidyUpSequenceData';
60
+ export { default as tidyUpAnnotation } from './tidyUpAnnotation';
61
+ export { default as condensePairwiseAlignmentDifferences } from './condensePairwiseAlignmentDifferences';
62
+ export { default as addGapsToSeqReads } from './addGapsToSeqReads';
63
+ export { default as calculateNebTm } from './calculateNebTm';
64
+ export { default as calculateNebTa } from './calculateNebTa';
65
+ export { default as getDigestFragmentsForCutsites } from './getDigestFragmentsForCutsites';
66
+ export { default as getDigestFragmentsForRestrictionEnzymes } from './getDigestFragmentsForRestrictionEnzymes';
67
+ export { default as convertDnaCaretPositionOrRangeToAA } from './convertDnaCaretPositionOrRangeToAA';
68
+ export { default as convertAACaretPositionOrRangeToDna } from './convertAACaretPositionOrRangeToDna';
69
+ export { default as aminoAcidToDegenerateDnaMap } from './aminoAcidToDegenerateDnaMap';
70
+ export { default as aminoAcidToDegenerateRnaMap } from './aminoAcidToDegenerateRnaMap';
71
+ export { default as degenerateDnaToAminoAcidMap } from './degenerateDnaToAminoAcidMap';
72
+ export { default as degenerateRnaToAminoAcidMap } from './degenerateRnaToAminoAcidMap';
73
+ export { default as getMassOfAaString } from './getMassOfAaString';
74
+ export { default as shiftAnnotationsByLen } from './shiftAnnotationsByLen';
75
+ export { default as adjustAnnotationsToInsert } from './adjustAnnotationsToInsert';
78
76
  export const FeatureTypes: any[];
79
77
  export const featureColors: {};
80
- import { autoAnnotate } from "./autoAnnotate";
81
- import { convertApELikeRegexToRegex } from "./autoAnnotate";
82
- import { convertProteinSeqToDNAIupac } from "./autoAnnotate";
83
78
  export { getFeatureToColorMap, getFeatureTypes, genbankFeatureTypes, getMergedFeatureMap, autoAnnotate, convertApELikeRegexToRegex, convertProteinSeqToDNAIupac };
84
- export { default as filterSequenceString, filterRnaString } from "./filterSequenceString";
79
+ export { default as filterSequenceString, filterRnaString } from './filterSequenceString';