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Created May 2, 2015 15:27
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file1.py
from biom import parse_table
with open('otu_table_hunter.biom') as f:
table = parse_table(f)
print table
table.ids()
table.ids(axis='observation')
table.nnz
normed = table.norm(axis='sample', inplace=False)
phylum_idx = 1
collapse_f = lambda id_, md: "; ".join(md['taxonomy'][:phylum_idx + 1])
collapsed = normed.collapse(collapse_f, axis='observation')
print collapsed
print collapsed
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