@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.
- package/DNAComplementMap.d.ts +1 -1
- package/addGapsToSeqReads.d.ts +3 -16
- package/adjustAnnotationsToInsert.d.ts +1 -2
- package/adjustBpsToReplaceOrInsert.d.ts +1 -2
- package/aliasedEnzymesByName.d.ts +1 -37
- package/aminoAcidToDegenerateDnaMap.d.ts +31 -1
- package/aminoAcidToDegenerateRnaMap.d.ts +1 -1
- package/annotateSingleSeq.d.ts +4 -5
- package/annotationTypes.d.ts +2 -2
- package/autoAnnotate.d.ts +8 -17
- package/bioData.d.ts +58 -10
- package/calculateEndStability.d.ts +1 -1
- package/calculateNebTa.d.ts +1 -6
- package/calculateNebTm.d.ts +4 -6
- package/calculatePercentGC.d.ts +1 -1
- package/calculateSantaLuciaTm.d.ts +114 -28
- package/calculateTm.d.ts +1 -13
- package/computeDigestFragments.d.ts +24 -30
- package/condensePairwiseAlignmentDifferences.d.ts +1 -1
- package/convertAACaretPositionOrRangeToDna.d.ts +1 -2
- package/convertDnaCaretPositionOrRangeToAA.d.ts +1 -2
- package/cutSequenceByRestrictionEnzyme.d.ts +1 -2
- package/defaultEnzymesByName.d.ts +1 -2
- package/degenerateDnaToAminoAcidMap.d.ts +1 -1
- package/degenerateRnaToAminoAcidMap.d.ts +1 -1
- package/deleteSequenceDataAtRange.d.ts +1 -2
- package/diffUtils.d.ts +7 -9
- package/doesEnzymeChopOutsideOfRecognitionSite.d.ts +1 -2
- package/featureTypesAndColors.d.ts +6 -19
- package/filterSequenceString.d.ts +10 -14
- package/findApproxMatches.d.ts +1 -7
- package/findNearestRangeOfSequenceOverlapToPosition.d.ts +1 -2
- package/findOrfsInPlasmid.d.ts +11 -2
- package/findSequenceMatches.d.ts +1 -11
- package/generateAnnotations.d.ts +1 -2
- package/generateSequenceData.d.ts +13 -8
- package/getAllInsertionsInSeqReads.d.ts +1 -11
- package/getAminoAcidDataForEachBaseOfDna.d.ts +5 -6
- package/getAminoAcidFromSequenceTriplet.d.ts +1 -1
- package/getAminoAcidStringFromSequenceString.d.ts +1 -3
- package/getCodonRangeForAASliver.d.ts +4 -3
- package/getComplementAminoAcidStringFromSequenceString.d.ts +1 -1
- package/getComplementSequenceAndAnnotations.d.ts +1 -5
- package/getComplementSequenceString.d.ts +1 -1
- package/getCutsiteType.d.ts +1 -2
- package/getCutsitesFromSequence.d.ts +1 -2
- package/getDegenerateDnaStringFromAAString.d.ts +1 -1
- package/getDegenerateRnaStringFromAAString.d.ts +1 -1
- package/getDigestFragmentsForCutsites.d.ts +1 -4
- package/getDigestFragmentsForRestrictionEnzymes.d.ts +1 -8
- package/getInsertBetweenVals.d.ts +1 -2
- package/getLeftAndRightOfSequenceInRangeGivenPosition.d.ts +1 -2
- package/getOrfsFromSequence.d.ts +11 -17
- package/getOverlapBetweenTwoSequences.d.ts +1 -2
- package/getPossiblePartsFromSequenceAndEnzymes.d.ts +1 -18
- package/getReverseAminoAcidStringFromSequenceString.d.ts +1 -1
- package/getReverseComplementAminoAcidStringFromSequenceString.d.ts +1 -1
- package/getReverseComplementAnnotation.d.ts +1 -11
- package/getReverseComplementSequenceAndAnnotations.d.ts +1 -5
- package/getReverseComplementSequenceString.d.ts +1 -1
- package/getReverseSequenceString.d.ts +1 -1
- package/getSequenceDataBetweenRange.d.ts +1 -9
- package/getVirtualDigest.d.ts +10 -11
- package/guessIfSequenceIsDnaAndNotProtein.d.ts +1 -5
- package/index.cjs +491 -728
- package/index.d.ts +5 -8
- package/index.js +491 -728
- package/index.umd.cjs +491 -728
- package/insertGapsIntoRefSeq.d.ts +1 -2
- package/insertSequenceDataAtPositionOrRange.d.ts +1 -10
- package/isEnzymeType2S.d.ts +1 -2
- package/mapAnnotationsToRows.d.ts +1 -9
- package/package.json +9 -12
- package/prepareCircularViewData.d.ts +1 -2
- package/prepareRowData.d.ts +3 -7
- package/proteinAlphabet.d.ts +1 -1
- package/rotateBpsToPosition.d.ts +1 -1
- package/rotateSequenceDataToPosition.d.ts +1 -3
- package/shiftAnnotationsByLen.d.ts +3 -4
- package/src/autoAnnotate.test.js +1 -0
- package/src/getSequenceDataBetweenRange.js +11 -2
- package/src/getSequenceDataBetweenRange.test.js +42 -0
- package/src/prepareRowData_output1.json +0 -1
- package/threeLetterSequenceStringToAminoAcidMap.d.ts +921 -11
- package/tidyUpAnnotation.d.ts +11 -13
- package/tidyUpSequenceData.d.ts +1 -15
- package/src/DNAComplementMap.ts +0 -32
- package/src/addGapsToSeqReads.ts +0 -436
- package/src/adjustAnnotationsToInsert.ts +0 -20
- package/src/adjustBpsToReplaceOrInsert.ts +0 -73
- package/src/aliasedEnzymesByName.ts +0 -7366
- package/src/aminoAcidToDegenerateDnaMap.ts +0 -32
- package/src/aminoAcidToDegenerateRnaMap.ts +0 -32
- package/src/annotateSingleSeq.ts +0 -37
- package/src/annotationTypes.ts +0 -23
- package/src/autoAnnotate.ts +0 -290
- package/src/bioData.ts +0 -65
- package/src/calculateEndStability.ts +0 -91
- package/src/calculateNebTa.ts +0 -46
- package/src/calculateNebTm.ts +0 -132
- package/src/calculatePercentGC.ts +0 -3
- package/src/calculateSantaLuciaTm.ts +0 -184
- package/src/calculateTm.ts +0 -242
- package/src/computeDigestFragments.ts +0 -238
- package/src/condensePairwiseAlignmentDifferences.ts +0 -85
- package/src/convertAACaretPositionOrRangeToDna.ts +0 -28
- package/src/convertDnaCaretPositionOrRangeToAA.ts +0 -28
- package/src/cutSequenceByRestrictionEnzyme.ts +0 -345
- package/src/defaultEnzymesByName.ts +0 -280
- package/src/degenerateDnaToAminoAcidMap.ts +0 -5
- package/src/degenerateRnaToAminoAcidMap.ts +0 -5
- package/src/deleteSequenceDataAtRange.ts +0 -13
- package/src/diffUtils.ts +0 -80
- package/src/doesEnzymeChopOutsideOfRecognitionSite.ts +0 -16
- package/src/featureTypesAndColors.ts +0 -167
- package/src/filterSequenceString.ts +0 -153
- package/src/findApproxMatches.ts +0 -58
- package/src/findNearestRangeOfSequenceOverlapToPosition.ts +0 -43
- package/src/findOrfsInPlasmid.ts +0 -31
- package/src/findSequenceMatches.ts +0 -154
- package/src/generateAnnotations.ts +0 -39
- package/src/generateSequenceData.ts +0 -212
- package/src/getAllInsertionsInSeqReads.ts +0 -100
- package/src/getAminoAcidDataForEachBaseOfDna.ts +0 -305
- package/src/getAminoAcidFromSequenceTriplet.ts +0 -27
- package/src/getAminoAcidStringFromSequenceString.ts +0 -36
- package/src/getCodonRangeForAASliver.ts +0 -73
- package/src/getComplementAminoAcidStringFromSequenceString.ts +0 -10
- package/src/getComplementSequenceAndAnnotations.ts +0 -25
- package/src/getComplementSequenceString.ts +0 -23
- package/src/getCutsiteType.ts +0 -18
- package/src/getCutsitesFromSequence.ts +0 -22
- package/src/getDegenerateDnaStringFromAAString.ts +0 -15
- package/src/getDegenerateRnaStringFromAAString.ts +0 -15
- package/src/getDigestFragmentsForCutsites.ts +0 -126
- package/src/getDigestFragmentsForRestrictionEnzymes.ts +0 -50
- package/src/getInsertBetweenVals.ts +0 -31
- package/src/getLeftAndRightOfSequenceInRangeGivenPosition.ts +0 -40
- package/src/getMassOfAaString.ts +0 -29
- package/src/getOrfsFromSequence.ts +0 -132
- package/src/getOverlapBetweenTwoSequences.ts +0 -30
- package/src/getPossiblePartsFromSequenceAndEnzymes.ts +0 -149
- package/src/getReverseAminoAcidStringFromSequenceString.ts +0 -22
- package/src/getReverseComplementAminoAcidStringFromSequenceString.ts +0 -10
- package/src/getReverseComplementAnnotation.ts +0 -33
- package/src/getReverseComplementSequenceAndAnnotations.ts +0 -46
- package/src/getReverseComplementSequenceString.ts +0 -18
- package/src/getReverseSequenceString.ts +0 -12
- package/src/getSequenceDataBetweenRange.ts +0 -154
- package/src/getVirtualDigest.ts +0 -139
- package/src/guessIfSequenceIsDnaAndNotProtein.ts +0 -39
- package/src/index.test.ts +0 -43
- package/src/index.ts +0 -111
- package/src/insertGapsIntoRefSeq.ts +0 -43
- package/src/insertSequenceDataAtPosition.ts +0 -2
- package/src/insertSequenceDataAtPositionOrRange.ts +0 -328
- package/src/isEnzymeType2S.ts +0 -5
- package/src/mapAnnotationsToRows.ts +0 -256
- package/src/prepareCircularViewData.ts +0 -24
- package/src/prepareRowData.ts +0 -61
- package/src/proteinAlphabet.ts +0 -271
- package/src/rotateBpsToPosition.ts +0 -12
- package/src/rotateSequenceDataToPosition.ts +0 -54
- package/src/shiftAnnotationsByLen.ts +0 -24
- package/src/threeLetterSequenceStringToAminoAcidMap.ts +0 -198
- package/src/tidyUpAnnotation.ts +0 -205
- package/src/tidyUpSequenceData.ts +0 -213
- package/src/types.ts +0 -109
- 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';
|