[UGENE-5972] Writing sequence names to a CSV file doesn't work for "Write Annotations" Created: 18/Jan/18  Updated: 07/Jul/18  Resolved: 12/Apr/18

Status: Closed
Project: UGENE
Component/s: Basic-Nucl, Workflow
Affects Version/s: 1.29
Fix Version/s: 1.30

Type: Bug Priority: Major
Reporter: Olga Golosova Assignee: Dmitrii Sukhomlinov
Resolution: Fixed  
Labels: request
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Attachments: Microsoft Word expected.csv     Microsoft Word seq_with_orfs.csv     Text File seq_with_orfs.fa    
Story Points: 3
Assigned Tester: Kirill Rasputin
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".

 Comments   
Comment by Olga Golosova [ 09/Apr/18 ]

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.
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