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  1. Jalview
  2. JAL-3529

UniProt accessions not written in Stockholm format from Pfam

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: 2.11.0
    • Fix Version/s: 2.11.1.0
    • Component/s: file format issue
    • Labels:
      None
    • Environment:
      Jalview Version: 2.11.0
      Jalview Installation: Source git-commit:a148aca2d [releases/Release_2_11_Branch]
      Build Date: 16:43:41 04 July 2019
      Java version: 1.8.0_202
      x86_64 Mac OS X 10.14.6

      Description

      If I fetch sequences from Pfam and then save as Stockholm format, the accessions aren't written correctly. In the #=GS AC I get the Pfam ID instead of the UniProt.

      Looks like this might be a general problem with writing accessions in Stockholm format. E.g., try fetching a sequence from UniProt and writing out to Stockholm.

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          Issue Links

          blocks

          Bug - A problem which impairs or prevents the functions of the product. JAL-3531 whitespace at beginning of database accessions parsed from Stockholm files

          • Major - Major loss of function.
          • Closed
          related with

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3532 Preserve pfam and rfam metadata when exporting retrieved entries as Stockholm

          • Major - Major loss of function.
          • Open

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              smacgowan Stuart MacGowan
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                Dates

                Created:
                Updated:
                Resolved: