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  1. UGENE
  2. UGENE-7901

Sanger alignment fails if path to files contains commas

    Details

    • Type: Bug
    • Status: Tested
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 50
    • Component/s: None
    • Labels:
      None
    • Sprint:
      DEV-48-3, DEV-48-4, DEV-48-5, DEV-48-RELEASE, DEV-49-1, DEV-49-2, DEV-49-3, DEV-49-4, DEV-49-5, DEV-49-RELEASE, DEV-50-1, DEV-50-2, DEV-50-3, DEV-50-4, DEV-50-5, DEV-50-RELEASE
    • Affect Type:
      Userdefined

      Description

      Scenario:

      1. Save sanger input files (e.g. from the "sanger" folder) to directory with commas "," in path.
      2. Click "Tools" -> "Sanger data analysis" -> "Maps reads to reference..." and run sanger with files, saved on 1. Declare only one file with reads.
        Expected: If you run the same alignment with the same files, located in a directory with comma-separated paths in Workflow Designer, the alignment passes without any problems. This makes me think, that commas (or maybe some other special characters, I haven't checked them all) do not influence the alignment process itself (here I need to remind you, that when you run Sanger alignment with the above-mentioned dialog, it runs in a child process). Probably, the problem appears on some process-preparation step. So, I expect, that this scenario should passes well and without failures after the fix you'll do. 
        Current: "wrong output format"

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          Issue Links

          is blocked by

          Bug - A problem which impairs or prevents the functions of the product. UGENE-7902 Unclear "wrong output format" when Sanger alignment fails

          • Major - Major loss of function.
          • Closed

            Activity

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            s.samoilenko Svetlana Samoilenko added a comment - - edited

            Scenario1: comma in the path

            1. Put reference and one read in the "Sanger,output" folder
            2. Click "Tools" -> "Sanger data analysis" -> "Maps reads to reference..." and run sanger with files
            3. Test passed

            Scenario2: *semicolon in the path

            1. Put reference and one read in the "Sanger;output" folder. It is possible to create folder with this name.
            2. Run "Maps reads to reference..." with these files
            3. Test failed: An error occurred. Process is not finished successfully.
              process:7760>Task {Workflow run from cmdline}

              finished with error: Map to Reference: 'D:/sanger' is not a file Map to Reference: File not found: 'D:/ugene/src/ugeneui/outpit/reference.gb' see 'ugene --help=align-to-reference' for details

            There may be cases when different files are placed in directories with different delimiters, some with commas, others with semicolons.

            Show
            s.samoilenko Svetlana Samoilenko added a comment - - edited Scenario1: comma in the path Put reference and one read in the "Sanger,output" folder Click "Tools" -> "Sanger data analysis" -> "Maps reads to reference..." and run sanger with files Test passed Scenario2: *semicolon in the path Put reference and one read in the "Sanger;output" folder. It is possible to create folder with this name. Run "Maps reads to reference..." with these files Test failed: An error occurred. Process is not finished successfully. process:7760>Task {Workflow run from cmdline} finished with error: Map to Reference: 'D:/sanger' is not a file Map to Reference: File not found: 'D:/ugene/src/ugeneui/outpit/reference.gb' see 'ugene --help=align-to-reference' for details There may be cases when different files are placed in directories with different delimiters, some with commas, others with semicolons.
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            yalgaer Yuliya Algaer added a comment -

            Задачу про точку с запятой делает Кирилл в рамках задачи UGENE-5291
            Его решение будет основано на этом же, но будет сложнее. Оно уже пойдет в следующий релиз.

            Show
            yalgaer Yuliya Algaer added a comment - Задачу про точку с запятой делает Кирилл в рамках задачи UGENE-5291 Его решение будет основано на этом же, но будет сложнее. Оно уже пойдет в следующий релиз.

              People

              Assignee:
              yalgaer Yuliya Algaer
              Reporter:
              dsukhomlinov Dmitrii Sukhomlinov
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: