Additional IPython format updates
Additional IPython format updates

Fixes syntax and functions calls

JWDebelius/American-Gut,JWDebelius/American-Gut,wasade/American-Gut,biocore/American-Gut,EmbrietteH/American-Gut,biocore/American-Gut,mortonjt/American-Gut,wasade/American-Gut,EmbrietteH/American-Gut