BIOM Table-codes

p { margin-bottom: 0.25cm; line-height: 120% }
a:link { }

import numpy

from biom.table import Table

============================================================================================================

# 10*4 matrix, [0, 39]

data = 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 = [{‘environment‘: ‘A‘}, {‘environment‘: ‘B‘},

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

observ_metadata = [{‘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)

============================================================================================================

data = 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).

============================================================================================================

============================================================================================================

p { margin-bottom: 0.25cm; line-height: 120% }
a:link { }