added KEGG Pathways metadata
Addresses Issue #58.  Inital commit of refactored code for loading a subset of a biom table.   Draws on biom library code.
Addresses Issue #58.  Inital commit modifying the script to load only the counts corresponding to OTUs that we want to make predictions about.
added categorize_by_function script
added new downstream analysis tutorial

this addresses issue #47
Merge pull request #61 from gregcaporaso/issue-47

added new downstream analysis tutorial
Adds test code for load_subset_from_biom_str and yield_subset_biom_str.  This currently passes EXCEPT for a case that fails due to incorrect parsing of fields containing commas.  The issue has been raised in the BIOM github project, so I'm leaving it for now, and note what's going on in the comment
Adds a commandline option to suppress the subset loader (for users with high-memory machines, where it might improve runtime on some tables)
Merge pull request #60 from wasade/categorize_by_function

added categorize_by_function script
Prevent error msg for loading biom files without .biom suffix

Addresses #63
Addresses Issue #62.  Test code for metagenome_contributions.py.
Addresses Issue #62.  Adds library code for a method for breaking down the contribution of individual organisms to a metagenome.
Addresses Issue #62.  Initial commit of a script for breaking down the contribution of individual organisms to a metagenome.
Minor tweaks to make sure function limitation is working
Merge pull request #57 from wasade/issue46

added KEGG Pathways metadata
Merge pull request #66 from zaneveld/metagenome_contributions

Metagenome contributions
Add tutorial files to github repository.

Addresses #35
Update metagenome prediction tutorial

Addresses #36
Allow creation of recursive directories for output
Change ancestral_state_reconstruction.py to use 'ace_pic' as default asr method.

Since PICRUSt uses 'ace_pic' method for producing precalculated files, the asr method should be set to the same default.