biom.table.Table.from_json

classmethod Table.from_json(json_table, data_pump=None, input_is_dense=False)

Parse a biom otu table type

Parameters:

json_tabledict

A JSON object or dict that represents the BIOM table

data_pumptuple or None

A secondary source of data

input_is_densebool

If True, the data contained will be interpretted as dense

Returns:

Table

Examples

>>> from biom import Table
>>> json_obj = {"id": "None",
...             "format": "Biological Observation Matrix 1.0.0",
...             "format_url": "http://biom-format.org",
...             "generated_by": "foo",
...             "type": "OTU table",
...             "date": "2014-06-03T14:24:40.884420",
...             "matrix_element_type": "float",
...             "shape": [5, 6],
...             "data": [[0,2,1.0],
...                      [1,0,5.0],
...                      [1,1,1.0],
...                      [1,3,2.0],
...                      [1,4,3.0],
...                      [1,5,1.0],
...                      [2,2,1.0],
...                      [2,3,4.0],
...                      [2,5,2.0],
...                      [3,0,2.0],
...                      [3,1,1.0],
...                      [3,2,1.0],
...                      [3,5,1.0],
...                      [4,1,1.0],
...                      [4,2,1.0]],
...             "rows": [{"id": "GG_OTU_1", "metadata": None},
...                      {"id": "GG_OTU_2", "metadata": None},
...                      {"id": "GG_OTU_3", "metadata": None},
...                      {"id": "GG_OTU_4", "metadata": None},
...                      {"id": "GG_OTU_5", "metadata": None}],
...             "columns": [{"id": "Sample1", "metadata": None},
...                         {"id": "Sample2", "metadata": None},
...                         {"id": "Sample3", "metadata": None},
...                         {"id": "Sample4", "metadata": None},
...                         {"id": "Sample5", "metadata": None},
...                         {"id": "Sample6", "metadata": None}]
...             }
>>> t = Table.from_json(json_obj)