@teselagen/sequence-utils 0.3.7 → 0.3.9
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 +1 -339
- package/filterSequenceString.d.ts +26 -1
- package/index.d.ts +7 -8
- package/index.js +329 -413
- package/index.mjs +329 -413
- package/index.umd.js +329 -413
- 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 +1 -366
- 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/filterSequenceString.js +111 -16
- package/src/filterSequenceString.test.js +62 -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 +79 -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 +31 -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 +15 -18
- package/filterAminoAcidSequenceString.d.ts +0 -1
- package/filterAminoAcidSequenceString.test.d.ts +0 -1
- package/src/filterAminoAcidSequenceString.js +0 -13
- package/src/filterAminoAcidSequenceString.test.js +0 -22
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@@ -1,12 +1,12 @@
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import { cloneDeep } from
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import { getYOffsetsForPotentiallyCircularRanges } from
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import { annotationTypes } from
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import { cloneDeep } from "lodash";
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import { getYOffsetsForPotentiallyCircularRanges } from "@teselagen/range-utils";
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import { annotationTypes } from "./annotationTypes";
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//basically just adds yOffsets to the annotations
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export default function prepareCircularViewData(sequenceData) {
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const clonedSeqData = cloneDeep(sequenceData);
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annotationTypes.forEach(
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if (annotationType !==
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annotationTypes.forEach(annotationType => {
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if (annotationType !== "cutsites") {
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const maxYOffset = getYOffsetsForPotentiallyCircularRanges(
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clonedSeqData[annotationType]
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).maxYOffset;
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package/src/prepareRowData.js
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// ac.throw([ac.posInt, ac.posInt, ac.bool], arguments);
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import mapAnnotationsToRows from "./mapAnnotationsToRows";
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@@ -38,4 +37,4 @@ export default function prepareRowData(sequenceData, bpsPerRow) {
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rows[rowNumber] = row;
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}
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return rows;
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}
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}
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