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Biopython deprecation warning. Biopython uses this warning instead of the built in DeprecationWarning since those are ignored by default since Python 2.7. To silence all our deprecation warning messages, use: >>> import warnings >>> from Bio import BiopythonDeprecationWarning >>> warnings.simplefilter('ignore', BiopythonDeprecationWarning) Code marked as deprecated is likely to be removed in a future version of Biopython. To avoid removal of this code, please contact the Biopython developers by sending an email to email@example.com.