UGENE
  1. UGENE
  2. UGENE-5972

Writing sequence names to a CSV file doesn't work for "Write Annotations"

    Details

    • Type: Bug Bug
    • Status: Closed Closed
    • Priority: Major Major
    • Resolution: Fixed
    • Affects Version/s: 1.29
    • Fix Version/s: 1.30
    • Component/s: Basic-Nucl, Workflow
    • Labels:
    • Story Points:
      3
    • Sprint:
      DEV-30-7
    • Affect Type:
      Userdefined

      Description

      Link: This is a request on UGENE forum.

      Scenario:

      1. Open the WD.
      2. Create the following workflow: "Read Sequence > ORF Marker > Write Annotations".
      3. Specify "seq_with_orfs.fa" inputfile in the "Read Sequence" element.
      4. Modify the "Write Annotations" element parameters as follows:
        • Set "Document format" to "CSV".
        • Set "Write sequence names" to "True".
      5. Run the workflow.
      6. Open the result "seq_with_orfs.csv" file.
        Current result: the file does not have "Sequence name" column.
        Expected result: there is "Sequence name" column after the "Complementary" column, see "expected.csv".
      1. expected.csv
        0.2 kB
        Olga Golosova
      2. seq_with_orfs.csv
        0.2 kB
        Olga Golosova
      3. seq_with_orfs.fa
        0.5 kB
        Olga Golosova

        Activity

        Hide
        Olga Golosova
        added a comment - - edited

        There may be the following use case for the "Write Annotations" element:

        • "Document format" is set to "CSV".
        • "Write sequence names" is "True".
        • Slot "Sequence" of the "Input annotations" port is NOT set.

        The expected behavior on a workflow run in this case should be the following:

        • Save the result with empty sequence names (i.e. the column is present, but the values are empty strings).
        • Show a warning on the dashboard:
          Sequence names were not saved, the input slot "Sequence" is empty.
          
        • Write an "ERROR" message into the log:
          Warning: sequence names were not saved, the input slot "Sequence" is empty.
          
        Show
        Olga Golosova
        added a comment - - edited There may be the following use case for the "Write Annotations" element: "Document format" is set to "CSV". "Write sequence names" is "True". Slot "Sequence" of the "Input annotations" port is NOT set. The expected behavior on a workflow run in this case should be the following: Save the result with empty sequence names (i.e. the column is present, but the values are empty strings). Show a warning on the dashboard: Sequence names were not saved, the input slot "Sequence" is empty. Write an "ERROR" message into the log: Warning: sequence names were not saved, the input slot "Sequence" is empty.

          People

          • Assignee:
            Dmitrii Sukhomlinov
            Reporter:
            Olga Golosova
            Assigned Tester:
            Kirill Rasputin
          • Votes:
            0 Vote for this issue
            Watchers:
            1 Start watching this issue

            Dates

            • Created:
              Updated:
              Resolved:

              Agile