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zstephens / neat-genreads

NEAT read simulation tools
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update deprecated biopython functions #104

Closed tturowski closed 1 year ago

tturowski commented 1 year ago

Using biopython 1.79 and higher raise error: AttributeError: 'Seq' object has no attribute 'tomutable' and AttributeError: 'MutableSeq' object has no attribute 'toseq'

to solve it four replacements are needed in SequenceContainer.py according to the biopython note: Instead of myseq.tomutable() or mymutableseq.toseq(), you should now use Bio.Seq.MutableSeq(myseq) or Bio.Seq.Seq(mymutableseq), respectively.

joshfactorial commented 1 year ago

Please use our most up to date repo at GitHub.com/NCSA/neat or downgrade to an older version of biopython for this repo.