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Export document fields to csv



  • Official comment
    Neil Bradley

    Hello Ida,

    It sounds like you are trying to extract fields from selected documents, which may include Sequence Lists as well as individual Sequence documents, via a Workflow.

    Step 1: Extract the sequences from the documents. This can be done by adding the step ‘For Each Sequence/Extract Sequences From List’.

    Step 2: Collating the sequences so that the next operation includes all of them. This can be done by then adding the step ‘Group Sequences’.

    Step 3: Exporting your fields to CSV. This can be done by then adding the Operation ‘Export’, and selecting the option ‘Expose all options’ will allow you to choose the fields you wish to export each time you use the workflow. You can also select default export fields via ‘Options’.

    Kind Regards,

    Neil (Prime Developer)

  • Ida Karlsson

    Hello Neil and thanks for the suggestions.
    When using 'Group Sequences' and 'Export' in a workflow I do get a csv file with data from all sequences. The problem is I am getting a file with the following header:

    Name # Source Sequences % Identical Sites % Pairwise Identity Command (BBDuk) Created Date Description Free end gaps Mean Coverage Modified Output (BBDuk) Read Technology Sample Sequence Sequence List Name Topology URN

    But what I selected in the export step was:

    # Source Sequences, Ambiguities, Mean Coverage, Sample
    How can I export these data instead?

  • Neil Bradley

    Hello Ida,

    Thank you for getting back to us again - sorry it has taken us so long to reply.

    Unfortunately, it turns out there is a bug in the Export to CSV function that means it always exports every field. This has been fixed upstream, however the fix is not scheduled for release until 2023.1, early next year.

    In the meantime, as this does not help you, we are working on a workflow to address this, and will hopefully post it here soon.

    Neil (Prime Developer).


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