import numpy

from biom.table import Table

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# 10*4 matrix, [0, 39]

data = http://www.mamicode.com/numpy.arange(40).reshape(10, 4)

sample_ids = [‘S%d‘ % i for i in range(4)]

observ_ids = [‘O%d‘ % i for i in range(10)]

sample_metadata = http://www.mamicode.com/[{‘environment‘: ‘A‘}, {‘environment‘: ‘B‘},

{‘environment‘: ‘A‘}, {‘environment‘: ‘B‘}]

observ_metadata = http://www.mamicode.com/[{‘taxonomy‘: [‘Bacteria‘, ‘Firmicutes‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Firmicutes‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Proteobacteria‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Proteobacteria‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Proteobacteria‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Bacteroidetes‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Bacteroidetes‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Firmicutes‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Firmicutes‘]},

{‘taxonomy‘: [‘Bacteria‘, ‘Firmicutes‘]}]

# construct table

table = Table(data, observ_ids, sample_ids, observ_metadata, sample_metadata, table_id=‘myTestTable‘)

# print info of table

table

print(table)

# print column names

print(table.ids())

print(table.ids(axis=‘sample‘))

# print row names

print(table.ids(axis=‘observation‘))

# print number of non-zero entries. Now it’s 39.

print(table.nnz)

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data = http://www.mamicode.com/numpy.asarray([[2, 0], [6, 1]])

table = Table(data, [‘O1‘, ‘O2‘], [‘S1‘, ‘S2‘])

# normalize by ‘sample’(column)

new_table = table.norm(inplace=False)

# normalize by row

new_table = table.norm(axis=‘observation‘, inplace=False)

# if inplace=True, table will change too. Now it stay unchanged. If set table1 = table before norm, and change table1 now, then table will change, too(shallow copy).

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BIOM Table-codes