[UGENE-7901] Sanger alignment fails if path to files contains commas Created: 03/Jul/23  Updated: 03/Apr/24  Resolved: 03/Apr/24

Status: Tested
Project: UGENE
Component/s: None
Affects Version/s: None
Fix Version/s: 50

Type: Bug Priority: Major
Reporter: Dmitrii Sukhomlinov Assignee: Yuliya Algaer
Resolution: Fixed  
Labels: None
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Issue Links:
Blocks
is blocked by UGENE-7902 Unclear "wrong output format" when Sa... Closed
Assigned Tester: Svetlana Samoilenko
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"

 Comments   
Comment by Svetlana Samoilenko [ 22/Mar/24 ]

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.

Comment by Yuliya Algaer [ 03/Apr/24 ]

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.

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