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can't parse multipart / jointed feature annotations, like CDS #6

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biosunsci opened this issue Sep 11, 2024 · 0 comments
Open

can't parse multipart / jointed feature annotations, like CDS #6

biosunsci opened this issue Sep 11, 2024 · 0 comments

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@biosunsci
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when trying to parse jointed feature file like in the src/example/genebank file RTO4_16460_joined_feature.gb,
results annotation only contains the first part of the CDs, like

CDS             join(1..59,168..272,338..484,571..580,692..935,1021..1184,
                     1250..1334,1402..1431,1509..1553,1617..1707,1790..1856)

is parsed into

"annotations": [
    {
      "direction": 1,
      "end": 59,
      "name": "RTO4_16460 CDS",
      "start": 0,
      "type": "CDS"
    }
  ],

the whole output is

{
  "annotations": [
    {
      "direction": 1,
      "end": 59,
      "name": "RTO4_16460 CDS",
      "start": 0,
      "type": "CDS"
    }
  ],
  "name": "No",
  "seq": "atgggccagcaggcgacgctcgaggagctgtacacacgctcagaaatctccaagatcaagcaagtcgagccagctcttctcctcaccaccccacaacataccccgcagcccacgacagctctcccacagcacccacagcctgctgaccagctcgagtgcatccacagatttgcgccctttggcgtcccgcggtcgcgccggctgcagacgttctccgtctttgcctggacgacggcactgcccatcctactcggcgtcttcttcctgctctggtgcgtcaggcttggcgtggattgggagtagcgggcgactcagctgacttgcgcatccgctccagctcgttcccaccgctctggccggccgtcatcgcctacctcacctgggtctttttcattgaccaggcgccgactcacggtggacgggcgcagtcttggctgcggaagagtcggatatgggtctggtttgcaggatattatcccgtcaggtgcgtcgtcccgtctgttgcgcgtcttgcgacctcgctcacggccaactcgcccgaccggctacctccgaacttcccgccaacagcttgatcaaggttcgtccacctttccttcagcttgagtgatctgtagaggagctgcaggatcaagcccaacccggggaggacctcggaggacgacgccgctgacttgctctcctcctacagagcgccgacttgccgcctgaccggaagtacgtcttcggctatcatccgcacggcgtcataggcatgggcgccatcgccaacttcgcgaccgacgcaaccggcttctcgacactcttccccggcttgaaccctcacctcctcaccctccaaagcaacttcaagctcccgctctatcgcgagttgctgctcgccctcggcatctgctccgtctcgatgaagagctgccagaacatcctgcggcaaggtgcgccagtcattccgaacgggcggtcgagcgtgaactctggggatgggaagagctgaccttctgcctcactccatccatgcaggtcctggctcggctctcaccatcgttgtcggtggcgcagccgagagcttgagtgcgcatcccggaaccgccgacctcacgctcaagcgacgaaaaggattcatcaagctcgcgatccggcaaggcgccgacctcgtgcccgtcttttcgttcggcgagaacgacgtgcgtcctctgctcgacttccgctagcgaagcccttcgctgacgctcccggtttcttcccccagatcttcggccagctgcgaaatgagcgagggacgcggctgtacaagttgcagaagcgtttccagggcgtattcggcttcactctccgtacgttgcgccgtgtcgcttcaatctgtcgagcgtccagtcgctcacgcagctacaactcccacagctctcttctacggtcggggactcttcaactgtacgcccgagtctacgtgactagtctaccgtgggaggcactgaagagcacggctgacgtcccacctctccgcgcagataacgttggcttgatgccgtaccgccatccgatcgtctcggtcggtgcgtcccccctcgtccctcctgacctgcgggcttcagctaacaattctcgacgacatctagtcggtcgaccaatctcggtgcagcagaaggaccacccaacgacagcggatctcgaagaagtccaggcgcggtatatcgcagaactcaagcggtgcgttccagacgtctacctttgcccgttgtctcagactcggtaagacagatcactgacgcttcggtcactggccgcgcagcatctgggaagactacaaggacgcctacgccaaaagtcgcacgcgggagctcaatattatcgcctga",
  "type": "dna"
}
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