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Allow setting sequenceType='pep' in ReferenceSequenceTrack configuration #4533

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merged 2 commits into from
Aug 27, 2024

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cmdcolin
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@cmdcolin cmdcolin commented Aug 26, 2024

This is a manually configured setting (e.g. not auto-detected from the fasta file) that lets a user configure a reference sequence to have a non-dna sequence type

This, if sequenceType!=='dna', then it disables the showTranslation/showForward/showReverse settings on the sequence track, and the "DNA coloring scheme" for the sequence letters. This works well for making a protein type browser

example screenshot

image

example config

{
      "name": "P05067",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "P05067-ReferenceSequenceTrack",
        "sequenceType": "pep", <-- this line
        "adapter": {
          "type": "UnindexedFastaAdapter",
          "fastaLocation": {
            "uri": "https://rest.uniprot.org/uniprotkb/P05067.fasta"
          }
        }
      }
    }

@cmdcolin cmdcolin changed the title Allow setting sequenceType='pep in ReferenceSequenceTrack configuration Allow setting sequenceType='pep' in ReferenceSequenceTrack configuration Aug 26, 2024
@cmdcolin
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of course, one could consider adding 'protein coloring schemes' on the reference sequence track, but there are many of these....

see also this related PR showing some protein browser demo data fetched from uniprot GMOD/jbrowse-plugin-protein3d#14

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