the command1 and command2 tests try to import the biom_format module, which doesn't exist. I assume the name is derived from the egg name, and thus the import fails.
work around: http://launchpadlibrarian.net/380438436/python-biom-format_2.1.6+dfsg-2build1_2.1.6+dfsg-2ubuntu1.diff.gz why do you need these tests, when you already have the unittests?
