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jbloomlab / dms_tools2

software for the analysis and visualization of deep mutational scanning data
GNU General Public License v3.0
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__init__.py file points to missing biopython module #50

Closed nguyenvanessa closed 3 years ago

nguyenvanessa commented 3 years ago

Hi Jesse,

When I try to import dms_tools2 into my Jupyter Notebook, I get an error: "'Bio.Seq' has no attribute 'IUPAC'".

The error occurs on line 55 of /dms_tools2/init.py. It looks like Biopython has moved ambiguous_dna_values to Bio.Data.IUPACData.ambiguous_DNA_values.

Changing this allowed me to import dms_tools2

jbloom commented 3 years ago

@nguyenvanessa, thanks for finding this. Do you want to make a pull request fixing it in code? Otherwise I can do it as well.

nguyenvanessa commented 3 years ago

I've made a pull request fixing this

jbloom commented 3 years ago

Merged in #51 and fixed in version 2.6.7. The cause of the issue was that the newest biopython (1.78) deprecated Bio.Seq.IUPAC.