Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-3841

Search in sequence regular expression annotation failure

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Cannot Reproduce
    • Affects Version/s: 1.15
    • Fix Version/s: None
    • Component/s: Basic-Nucl
    • Labels:
    • Sprint:
      DEV-39-5
    • Affect Type:
      Userdefined

      Description

      Issue exists of several components:

      1) While searching for a pattern within a sequence, regular expressions cannot be entered in the 'search for' input field. Not all characters (e.g. numbers) seem to be allowed, making it for example impossible to enter a full regular expression such as AGTAGC.

      {30,35}GGTACG. Only AGTAGC.{,}GGTACG without range is displayed instead. Input of this kind of regular expressions does seem to be allowed when loaded from a file.

      2) Searching with regular expressions containing a range, such as AGTAGC.{30,35}

      GGTACG mentioned above, sometimes result into failure of finding several exact hits, which do meet all of the conditions provided. Tested using several regex searches in UGene compared with IGV Browser. May be related to ranges such as

      {30,35} and/or other regular expressions not being interpreted correctly by Ugene.

      3) After searching for a regular expression loaded from a file, such as AGTAGC.{30,35}

      GGTACG, the hits are shown in the search panel. Creating annotations results only into adding the provided annotations table name to the project. The created .gb file is blank however, and no hits are present in the added project annotation file either.

      4) UGene freezes without recovery when searching for many regular expression patterns while altering the parameters, since the search is already initiated after a change is detected. Adding an option to toggle auto-search on/off might prevent this freezing.

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              biserova Evelina
              Reporter:
              MichielMunckhof Michiel van den Munckhof
              Assigned Tester:
              Dmitrii Sukhomlinov
              Watchers:
              4 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: