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  1. UGENE
  2. UGENE-6781

GTF parsing errors for GTF from UCSC with additional whitespace characters

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 34
    • Fix Version/s: 35
    • Component/s: Basic-Nucl
    • Labels:
    • Story Points:
      3
    • Epic Link:
    • Sprint:
      DEV-35-2
    • Affect Type:
      Userdefined

      Description

      See the attached "chr1-10000-lines.gtf" file. This data were downloaded from UCSC and should be considered as valid. However, UGENE outputs a lot of messages into the log like:

      [TRACE] GTF parsing error: invalid attributes format at line 9950!
      

      And an error message:

      [ERROR]GTF parsing error: one or more errors occurred while parsing the input file, see TRACE log for details!
      

      It seems the problem is additional space characters in a line. Fix the issue in a similar way as UGENE-6406, i.e. open the file without errors, however write the following INFO message:

      The 'file_name' file GTF format is not strict — there are unexpected whitespace characters in some lines.
      

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              Assignee:
              kir Kirill Rasputin
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
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                Dates

                Created:
                Updated:
                Resolved: