Replace Biopython trie with pygtrie

fhcrc / seqmagick

An imagemagick-like frontend to Biopython SeqIO

http://seqmagick.readthedocs.org

GNU General Public License v3.0

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Replace Biopython trie with pygtrie #86

Closed nileshpatra closed 4 years ago

nileshpatra commented 4 years ago

Biopython's trie and triefind Modules are deprecated. This is an attempt to replace the functionality with pygtrie. Fixes: #84

It also seems that Biopython support has been dropped for python-3.5 as can be seen in the Python Requirements section here This is further confirmed as the latest commit in the master branch also fails the travis test, the result o which can be seen here

This is an attempt to fix it.

matsen commented 4 years ago

@jgallowa07 if you are happy, then please merge!

We'll have to see what the state of the PyPI upload is after that.

jgallowa07 commented 4 years ago

@matsen I don't have write access to this repo atm.