@teselagen/sequence-utils 0.3.7 → 0.3.8
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/README.md +89 -0
- package/bioData.d.ts +0 -339
- package/index.d.ts +7 -7
- package/index.js +238 -384
- package/index.mjs +238 -384
- package/index.umd.js +238 -384
- package/package.json +1 -2
- package/src/addGapsToSeqReads.js +2 -2
- package/src/adjustAnnotationsToInsert.js +3 -3
- package/src/adjustBpsToReplaceOrInsert.js +3 -3
- package/src/adjustBpsToReplaceOrInsert.test.js +0 -1
- package/src/aminoAcidToDnaRna.test.js +1 -1
- package/src/annotateSingleSeq.js +1 -1
- package/src/annotateSingleSeq.test.js +1 -4
- package/src/autoAnnotate.js +5 -2
- package/src/autoAnnotate.test.js +6 -30
- package/src/bioData.js +0 -365
- package/src/calculateNebTa.js +1 -1
- package/src/calculateNebTm.js +1 -1
- package/src/calculatePercentGC.js +2 -2
- package/src/calculateTm.js +19 -102
- package/src/computeDigestFragments.js +7 -4
- package/src/computeDigestFragments.test.js +1 -1
- package/src/condensePairwiseAlignmentDifferences.js +1 -1
- package/src/convertAACaretPositionOrRangeToDna.js +1 -1
- package/src/convertDnaCaretPositionOrRangeToAA.js +1 -1
- package/src/cutSequenceByRestrictionEnzyme.js +3 -3
- package/src/cutSequenceByRestrictionEnzyme.test.js +0 -1
- package/src/degenerateDnaToAminoAcidMap.js +1 -1
- package/src/degenerateRnaToAminoAcidMap.js +1 -1
- package/src/deleteSequenceDataAtRange.js +1 -1
- package/src/deleteSequenceDataAtRange.test.js +23 -9
- package/src/diffUtils.js +4 -4
- package/src/diffUtils.test.js +2 -2
- package/src/doesEnzymeChopOutsideOfRecognitionSite.js +1 -1
- package/src/doesEnzymeChopOutsideOfRecognitionSite.test.js +0 -2
- package/src/featureTypesAndColors.js +5 -5
- package/src/featureTypesAndColors.test.js +1 -1
- package/src/filterAminoAcidSequenceString.js +4 -7
- package/src/filterAminoAcidSequenceString.test.js +3 -1
- package/src/filterSequenceString.js +5 -3
- package/src/findNearestRangeOfSequenceOverlapToPosition.js +1 -1
- package/src/findOrfsInPlasmid.js +1 -1
- package/src/findSequenceMatches.js +9 -10
- package/src/generateAnnotations.js +1 -1
- package/src/generateSequenceData.js +1 -1
- package/src/generateSequenceData.test.js +1 -1
- package/src/getAllInsertionsInSeqReads.js +1 -1
- package/src/getAminoAcidDataForEachBaseOfDna.js +2 -2
- package/src/getAminoAcidDataForEachBaseOfDna.test.js +0 -2
- package/src/getAminoAcidFromSequenceTriplet.js +1 -1
- package/src/getAminoAcidStringFromSequenceString.js +1 -1
- package/src/getCodonRangeForAASliver.js +1 -1
- package/src/getComplementAminoAcidStringFromSequenceString.js +2 -5
- package/src/getComplementSequenceAndAnnotations.js +1 -2
- package/src/getComplementSequenceString.js +5 -3
- package/src/getComplementSequenceString.test.js +6 -6
- package/src/getCutsiteType.js +1 -1
- package/src/getCutsitesFromSequence.js +1 -1
- package/src/getDegenerateDnaStringFromAAString.js +1 -1
- package/src/getDegenerateRnaStringFromAAString.js +1 -1
- package/src/getDigestFragmentsForCutsites.js +5 -2
- package/src/getDigestFragmentsForRestrictionEnzymes.js +2 -2
- package/src/getInsertBetweenVals.js +2 -2
- package/src/getLeftAndRightOfSequenceInRangeGivenPosition.js +2 -2
- package/src/getLeftAndRightOfSequenceInRangeGivenPosition.test.js +0 -2
- package/src/getMassOfAaString.js +4 -1
- package/src/getMassofAaString.test.js +9 -8
- package/src/getOrfsFromSequence.js +1 -2
- package/src/getOrfsFromSequence.test.js +1 -3
- package/src/getOverlapBetweenTwoSequences.js +3 -3
- package/src/getOverlapBetweenTwoSequences.test.js +1 -1
- package/src/getPossiblePartsFromSequenceAndEnzymes.js +2 -2
- package/src/getReverseAminoAcidStringFromSequenceString.js +1 -1
- package/src/getReverseComplementAminoAcidStringFromSequenceString.js +9 -6
- package/src/getReverseComplementAnnotation.js +1 -1
- package/src/getReverseComplementSequenceAndAnnotations.js +2 -3
- package/src/getReverseComplementSequenceString.js +1 -2
- package/src/getReverseSequenceString.js +1 -1
- package/src/getSequenceDataBetweenRange.js +7 -4
- package/src/getSequenceDataBetweenRange.test.js +0 -1
- package/src/getVirtualDigest.js +6 -3
- package/src/guessIfSequenceIsDnaAndNotProtein.js +2 -2
- package/src/index.js +80 -80
- package/src/index.test.js +5 -4
- package/src/insertGapsIntoRefSeq.js +1 -1
- package/src/insertSequenceDataAtPosition.test.js +4 -2
- package/src/insertSequenceDataAtPositionOrRange.js +5 -5
- package/src/insertSequenceDataAtPositionOrRange.test.js +3 -17
- package/src/isEnzymeType2S.js +1 -1
- package/src/mapAnnotationsToRows.js +3 -3
- package/src/mapAnnotationsToRows.test.js +1 -3
- package/src/prepareCircularViewData.js +5 -5
- package/src/prepareCircularViewData.test.js +1 -1
- package/src/prepareRowData.js +1 -2
- package/src/prepareRowData.test.js +1 -3
- package/src/prepareRowData_output1.json +381 -381
- package/src/proteinAlphabet.js +34 -26
- package/src/rotateBpsToPosition.js +7 -11
- package/src/rotateBpsToPosition.test.js +6 -6
- package/src/rotateSequenceDataToPosition.js +4 -4
- package/src/shiftAnnotationsByLen.js +2 -2
- package/src/tidyUpAnnotation.js +8 -7
- package/src/tidyUpSequenceData.js +3 -3
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|
-
"end": 15,
|
|
369
|
-
"yOffset": 0,
|
|
370
|
-
"enclosingRangeType": "beginning"
|
|
371
|
-
}
|
|
372
|
-
],
|
|
373
|
-
"translations": [],
|
|
374
|
-
"primers": [
|
|
375
|
-
{
|
|
376
|
-
"id": "b",
|
|
377
|
-
"annotation": {
|
|
378
|
-
"start": 10,
|
|
379
|
-
"end": 4,
|
|
380
|
-
"id": "b"
|
|
381
|
-
},
|
|
382
|
-
"start": 15,
|
|
383
|
-
"end": 15,
|
|
384
|
-
"yOffset": 0,
|
|
385
|
-
"enclosingRangeType": "beginning"
|
|
386
|
-
}
|
|
387
|
-
],
|
|
388
|
-
"guides": [],
|
|
389
|
-
"sequence": "a"
|
|
390
|
-
}
|
|
384
|
+
"yOffset": 0,
|
|
385
|
+
"enclosingRangeType": "beginning"
|
|
386
|
+
}
|
|
387
|
+
],
|
|
388
|
+
"guides": [],
|
|
389
|
+
"sequence": "a"
|
|
390
|
+
}
|
|
391
391
|
]
|