Thanks @devonorourke,
Yeah I recall our last encounter with this. It still baffles me that a sequence repository would not follow standard IUPAC rules for sequence deposition. This issue crops up from time to time with others too.
It might be worth considering replacing Is with Ns, with a replace_non_iupac_with_Ns method. In the short term, users can try bioawk:
bioawk -c fastx 'gsub("I", "N") $seq {print ">" $name; print $seq}' < infile.fasta > outfile.fasta
-Mike