biocore/qiime — pull request #1472 by ElBrogrammer (2014-03-27 18:38:32+00:00)
Title: update to use skbio's degeneracy expander

Uses `skbio.core.sequence.DNASequence.nondegenerates` in place of PyCogent's `SequenceGenerator` to expand degenerate primers.

The new skbio sequence objects will work with upper or lowercase sequences, as well as gap characters. It also preserves case. For example, expanding `Aka.-` will expand to `Ata.-` and `Aga.-`. @walterst do you see any issues with this? I'm not familiar with the split_libraries.py code, so not sure where additional validation (if any) should go.