Important: This documentation covers Yarn 1 (Classic).
For Yarn 2+ docs and migration guide, see yarnpkg.com.

Package detail

ve-sequence-utils

TeselaGen3.8kMITdeprecated5.2.16

ve-sequence-utils has moved to @teselagen/sequence-utils

sequence utility functions

sequence, dna, enzyme, digest, aminoacid, utils, teselagen, biojs

readme

CHANGELOG

About this Repo

This is a collection of dna sequence utility functions.

All sequences and annotations (unless otherwise specified) are assumed to have 0-based inclusive indices.

  Example:
  0123456
  ATGAGAG
  --fff--  (the feature covers GAG)
  0-based inclusive start:
  feature.start = 2
  1-based inclusive start:
  feature.start = 3
  0-based inclusive end:
  feature.end = 4
  1-based inclusive end:
  feature.end = 5

Editing This Repo:

All collaborators:

Edit/create a new file and update/add any relevant tests. Make sure they pass by running npm test

Updating this repo:

Commit and push all changes first (make sure tests are passing!)

Teselagen collaborators:

Commit and push all changes Sign into npm using the teselagen npm account (npm whoami)

npm version patch|minor|major
npm publish

Outside collaborators:

fork and pull request please :)

changelog

Changelog

All notable changes to this project will be documented in this file. Dates are displayed in UTC.

Generated by auto-changelog.

v5.2.16

  • exporting generateAnnotations 335ece9

v5.2.15

14 March 2023

  • speeding up tidyUpAnnotation by passing featureTypes from tidyUpSequenceData 6e0ea2d

v5.2.14

28 February 2023

  • fix undefined global in browser #201

v5.2.13

28 February 2023

v5.2.12

27 February 2023

  • updating version of node used in CI 916c205

v5.2.11

27 February 2023

  • updating getVirtualDigest to take a couple more options cc9908a

v5.2.10

27 February 2023

  • updating getVirtualDigest to take a couple more options 045a8e6

v5.2.9

9 December 2022

  • adding one more check for updating circularity bca474e

v5.2.8

17 November 2022

  • updating BsaMI to not be a typeIIS since it isn't quite one 089c38e

v5.2.7

16 November 2022

  • adding a bit more logic to dna circularity check b70b03a

v5.2.6

15 November 2022

  • adding convertProteinSeqToDNAIupac function 797307f
  • adding an additional test 9564225

v5.2.5

9 November 2022

  • adding isOverridden flag to features that have been overridden 9c1d096

v5.2.4

9 November 2022

  • adding includeHidden option to getFeatureToColorMap and getFeatureTypes bb04bb5
  • adding isOverridden flag to features that have been overridden 1ca2486

v5.2.3

8 November 2022

  • updating featureTypesAndColors and tests 90279fb

v5.2.1

7 November 2022

  • updating feature type handling a8b6134

v5.2.0

4 November 2022

  • adding a new getter for feature types and colors to allow passing additional types bcde08d

v5.1.38

3 October 2022

  • adding includeOverAndUnderHangs option to computeDigestFragments 65dfc90

v5.1.37

29 September 2022

  • adding values for O and U AAs for protein_letters_1to3 e669910

v5.1.36

13 September 2022

  • fixing computeDigestFragments for linear seqs w no cutsites 53f5c76

v5.1.35

7 September 2022

  • adding computeDigestFragments and getDigestFragsForSeqAndEnzymes functions 7c15d45

v5.1.34

16 August 2022

  • updating tidyUpAnnotation.js to auto-parse annotation.notes into JSON and gracefully handle errors c8821b9

v5.1.33

10 August 2022

  • adding U to the guess if sequence is protein check a468409

v5.1.32

4 August 2022

v5.1.31

4 August 2022

  • still trying to fix window issue 0813a15

v5.1.30

4 August 2022

v5.1.29

2 August 2022

  • adding a shiftAnnotationsByLen function 15b53ba
  • updating getSequenceDataBetweenRange to remove filtered annotations fd75f1e

v5.1.27

29 July 2022

  • adding a loose mode to guessIfSequenceIsDnaAndNotProtein 02aa24c

v5.1.26

29 July 2022

  • Added Get Mass of Aa String #200
  • Update version 5.1.24 #199
  • Added Molecular Mass to Alphabet #198
  • added molecular weights to alphabet e653cf9
  • changed weight to mass f3663d9
  • added weights for non-aa's 713ec9f

v5.1.23

7 July 2022

  • updating generateSequenceData to pass annotation numbers e0a90fa

v5.1.22

17 June 2022

v5.1.21

17 June 2022

v5.1.20

15 June 2022

  • adding option to filter off CDS translations to tidyUpSequenceData 0f9ffcf

v5.1.18

15 June 2022

v5.1.17

15 June 2022

  • reverting reverse sequence string c6d714c

v5.1.16

19 May 2022

  • Adding in a Reverse Function #197
  • adding reverseSequenceString fn 3c4660b

v5.1.14

13 January 2022

  • updating primer mapping to split primers above and below the sequence instead of mapping them all to be above ccab5ef

v5.1.13

20 December 2021

  • updating to improve baseCalls handling with chromatogramData editing be73ee0
  • adding a homepage link to package.json f1b706a

v5.1.12

11 November 2021

  • adding in chromatogramData insert/delete/update handling 98c8279

v5.1.11

20 October 2021

  • improving coloring of proteinAlphabet hydrophobicity scale 411576a

v5.1.10

19 October 2021

  • fixing tidyUpAnnotation logic and adding a test 1d37492

v5.1.9

19 October 2021

  • adding doNotProvideIdsForAnnotations flag for tidyUpSequencData; adding alternate colorByFamily colors to amino acids edad0ce

v5.1.8

13 October 2021

  • updating npmignore and annotateSingleSeq export pattern a32306b

v5.1.7

13 October 2021

  • adding an annotateSingleSeq function 02316fa

v5.1.6

23 September 2021

  • updating deps; removing validate.io-nonnegative-integer-array e5e0f6d

v5.1.5

17 September 2021

  • update aminoAcidToDegenerateDnaMap.js and add aminoAcidToDegenerateRnaMap.js #196
  • CLN-32292: update aminoAcidToDegenerateDnaMap.js b5d0b49
  • update 31e19e1

v5.1.4

16 August 2021

  • updating getSequenceDataBetweenRange to properly handle annotations that overlap themselves d846f2d

v5.1.3

11 August 2021

  • updating mapAnnotationsToRows to handle overlapsSelf flag 6e34bd6

v5.1.2

9 August 2021

  • updating getSequenceDataBetweenRange to handle range.overlapsSelf flag 81bafbe
  • Merge pull request #194 from TeselaGen/dependabot/npm_and_yarn/tar-4.4.15 0e2af20
  • [Security] Bump tar from 4.4.8 to 4.4.15 9b7e9d0

v5.1.1

29 June 2021

  • adding autoAnnotate and convertApELikeRegexToRegex 8027d0d
  • Merge pull request #176 from TeselaGen/dependabot/npm_and_yarn/npm-check-5.9.2 40e0e6c
  • Bump npm-check from 5.9.0 to 5.9.2 cb190b2

v5.0.2

17 March 2021

v5.0.1

15 March 2021

  • [Security] Bump mixin-deep from 1.3.1 to 1.3.2 #27
  • added ve-range-utils version with flipContainedRange bug fix...added … #10
  • Aligningshortseqreads #9
  • Added more feature types #8
  • Added U to filterAminoAcidSequenceString #6
  • Add option for to include stop codon #1
  • fixing issue with location copying in getSequenceDataBetweenRange and adding tests; links https://github.com/TeselaGen/openVectorEditor/issues/634 af6d514
  • Merge pull request #154 from TeselaGen/dependabot/npm_and_yarn/elliptic-6.5.4 df7f203
  • adding aliasedEnzymesByName and defaultEnzymesByName; removing old enzymeList a9fa562

1.0.8

2 March 2016

  • added t as acceptable amino acid char 03c3dc4

1.0.7

2 March 2016

  • updating gitignore, adding test file ea7e125
  • added x as an acceptable AA char 443bcb2

1.0.6

1 March 2016

  • removing api-checks, adding ids to annotations by default in tidyUpSequenceData d87b98a

1.0.5

10 February 2016

  • fixing es6 incompatibilities b894843

1.0.4

10 February 2016

1.0.3

10 February 2016

1.0.2

10 February 2016

  • moving to Teselagen's github afbc761
  • fixing tests, adding gitignore fa359f4