UGENE
  1. UGENE
  2. UGENE-6591

Parsing of LOCUS line in GenBank should be token-based

    Details

    • Type: Bug Bug
    • Status: Open Open
    • Priority: Trivial Trivial
    • Resolution: Unresolved
    • Affects Version/s: 1.32
    • Fix Version/s: None
    • Component/s: Basic-Nucl, Basic-Phy
    • Labels:
    • Affect Type:
      Userdefined

      Description

      Currently, data specified in the LOCUS line must start from position 13 in the UGENE implementation of the GenBank format. However, it is not essential according to the GenBank format specification (ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt):

      3.4.4 LOCUS Format
      3.4.4.1 : Important notice about parsing the LOCUS line
      Users who process the data elements of the LOCUS line should use a
      token-based parsing approach rather than parsing its content based on
      fixed column positions.

      When a file is read, implement a token-based, not positional, parting of the LOCUS line. On writing a GenBank file keep the historical indentation, if possible.

      1. gbrel.txt
        393 kB
        Olga Golosova

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          • Assignee:
            Unassigned
            Reporter:
            Olga Golosova
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            Dates

            • Created:
              Updated: