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  1. Jalview
  2. JAL-3660

Jalview does not honour file format when exporting file as new format via command line

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 2.10.2, 2.10.2b1, 2.10.2b2, 2.10.3, 2.10.3b1, 2.10.4, 2.10.4b1, 2.10.5, 2.11.0, 2.11.1.0
    • Fix Version/s: 2.11.1_js, 2.11.1.1, 2.11.2, 2.12.0
    • Component/s: Command Line Interface
    • Labels:
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      Description

      jalview.bin.Jalview.doMain ignores all the flat file output format options listed in its help :
      -fasta FILE Create alignment file FILE in Fasta format.
      -clustal FILE Create alignment file FILE in Clustal format.
      -pfam FILE Create alignment file FILE in PFAM format.
      -msf FILE Create alignment file FILE in MSF format.
      -pileup FILE Create alignment file FILE in Pileup format
      -pir FILE Create alignment file FILE in PIR format.
      -blc FILE Create alignment file FILE in BLC format.
      -json FILE Create alignment file FILE in JSON format.
      -jalview FILE Create alignment file FILE in Jalview format.
      -png FILE Create PNG image FILE from alignment.
      -svg FILE Create SVG image FILE from alignment.
      -html FILE Create HTML file from alignment.
      -biojsMSA FILE Create BioJS MSA Viewer HTML file from alignment.
      -imgMap FILE Create HTML file FILE with image map of PNG image.
      -eps FILE Create EPS file FILE from alignment.

      It just writes out the file in the format used to import it.

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              Assignee:
              jprocter Jim Procter
              Reporter:
              hansonr Bob Hanson
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                Created:
                Updated:
                Resolved: