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  1. Jalview
  2. JAL-2425

Pfam seed and full alignment retrieval does not have alignment metadata

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: 2.10.1
    • Fix Version/s: 2.10.2
    • Labels:
      None
    • Urgency:
      Nice to have

      Description

      Pfam (and possibly other Xfam dbs) have changed the way their alignment download api works. In 2.10.1, we retrieved the raw stockholm files with this base URL:
      http://pfam.xfam.org/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry=

      Now, this URL redirects to
      http://pfam.xfam.org/family/PF03760/alignment/seed/format?format=stockholm&alnType=seed&order=t&case=l&gaps=default

      Which serves a stockholm file without the metadata on the seed, and how it was constructed (hmmbuild options, date, etc), that is normally shown in the Alignment Properties window.

      Simply removing the parameters gives the complete stockholm file:
      http://pfam.xfam.org/family/PF03760/alignment/seed

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Created:
                Updated:
                Resolved: