Details
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Type: Bug
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Status: Closed
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Priority: Minor
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Resolution: Fixed
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Affects Version/s: 2.10.1
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Fix Version/s: 2.10.2
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Component/s: data retrieval services
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Labels:None
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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
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