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  1. UGENE
  2. UGENE-6628

Empty sequences should not be added to the alignment

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 33
    • Fix Version/s: 34
    • Component/s: Basic-MSA
    • Labels:
    • Story Points:
      3
    • Sprint:
      DEV-34-3, DEV-34-4, DEV-34-5
    • Affect Type:
      Userdefined

      Description

      Scenario 1: aligning to this alignment of several sequences, some of which contain only gaps

      1. Open "COI.aln" file.
      2. Click "Align sequence(s) to this alignment" button on the Alignment Editor toolbar.
      3. Select "_common_data\empty_sequences\multifasta_with_gap_seq.fa".
        Current result: all sequences are aligned, "seq2" and "seq4" consists of gaps only. There are no any notifications.
        Expected result: sequences made of gaps only are not aligned, i.e. "seq1", "seq3" and "seq5" are aligned. Also, a warning notification appears:
        The following sequence(s) were not aligned as they do not contain meaningful characters: "seq2", "seq4".
        

      Scenario 2: aligning to this alignment of a sequence with gaps only

      1. Open "COI.aln" file.
      2. Click "Align sequence(s) to this alignment" button on the Alignment Editor toolbar.
      3. Select "_common_data\empty_sequences\gap_only_seq.fa".
        Current result: the "gap-only-sequence" row is added to the alignment, it consists of gaps only. There are no any notifications.
        Expected result: the alignment is not modified. A warning notification appears:
        The following sequence(s) were not aligned as they do not contain meaningful characters: "gap-only-sequence".
        

      Scenario 3: aligning to this alignment a file without characters at all

      1. Open "COI.aln" file.
      2. Click "Align sequence(s) to this alignment" button on the Alignment Editor toolbar.
      3. Select "_common_data\empty_sequences\empty_file.fa".
        Current result: the COI alignment is not modified, an error notification appears:
        'Load sequences and add to alignment task' task failed: Unknown format
        

        Expected result: the COI alignment is not modified, but the error notification is the following:

        Data from the "empty-file.fa" file can't be alignment to the "COI" alignment - the file is empty.
        

      Scenario 4: aligning to this alignment an incorrect FASTA file that contains a header, but not a sequence

      1. Open "COI.aln" file.
      2. Click "Align sequence(s) to this alignment" button on the Alignment Editor toolbar.
      3. Select "_common_data\empty_sequences\incorrect_fasta_header_only.fa".
        Current result: the COI alignment is not modified, an error notification appears:
        'Load sequences and add to alignment task' task failed: Document is empty.
        

        Expected result: the COI alignment is not modified, but an error notification is the following:

        Data from the "empty-file.fa" file can't be alignment to the "COI" alignment - the file format is invalid.
        

      Scenario 5:
      The same as Scenario 4, but use "incorrect_multifasta_with_empty_seq.fa" instead of "incorrect_fasta_header_only.fa". Make sure "seq1" is not aligned in this case!

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              Assignee:
              dsukhomlinov Dmitrii Sukhomlinov
              Reporter:
              s.samoilenko Svetlana Samoilenko
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
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                Dates

                Created:
                Updated:
                Resolved: