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Please replace deprecated module Bio.triefind #84

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tillea opened this issue Jun 22, 2020 · 2 comments · Fixed by #86
Closed

Please replace deprecated module Bio.triefind #84

tillea opened this issue Jun 22, 2020 · 2 comments · Fixed by #86

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@tillea
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tillea commented Jun 22, 2020

Hi,
quoting Biopython deprecation documentation:

Bio.trie, Bio.triefind
These modules were declared obsolete in Release 1.72, deprecated in
Release 1.73, and removed in Release 1.77. We suggest pygtrie as an
alternative library implementing a trie data structure.

Unfortunately seqmagick is using Bio.triefind which raises an error in its build time test when building with latest Biopython (see bug report in Debian )

Kind regards, Andreas.
@tillea
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tillea commented Jul 6, 2020

Any comment on this?

@matsen
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matsen commented Jul 7, 2020

We're busy right now but it's on the todo list for a programmer in the group.

This was referenced Aug 16, 2020
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Replace Biopython trie with pygtrie nileshpatra/seqmagick
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@matsen @tillea