f = open('test.biom','w')
f.write("""{
    "columns": [
        {
            "id": "Sample1",
            "metadata": {
                "BarcodeSequence": "AGCACGAGCCTA",
                "DOB": 20060805
            }
        },
        {
            "id": "Sample2",
            "metadata": {
                "BarcodeSequence": "AACTCGTCGATG",
                "DOB": 20060216
            }
        },
        {
            "id": "Sample3",
            "metadata": {
                "BarcodeSequence": "ACAGACCACTCA",
                "DOB": 20060109
            }
        },
        {
            "id": "Sample4",
            "metadata": {
                "BarcodeSequence": "ACCAGCGACTAG",
                "DOB": 20070530
            }
        },
        {
            "id": "Sample5",
            "metadata": {
                "BarcodeSequence": "AGCAGCACTTGT",
                "DOB": 20070101
            }
        },
        {
            "id": "Sample6",
            "metadata": {
                "BarcodeSequence": "AGCAGCACAACT",
                "DOB": 20070716
            }
        }
    ],
    "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]
    ],
    "date": "2012-12-11T07:30:29.870689",
    "format": "Biological Observation Matrix 1.0.0",
    "format_url": "http://biom-format.org",
    "generated_by": "some software package",
    "id": null,
    "matrix_element_type": "float",
    "matrix_type": "sparse",
    "rows": [
        {
            "id": "GG_OTU_1",
            "metadata": {
                "confidence": 0.665,
                "taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]
            }
        },
        {
            "id": "GG_OTU_2",
            "metadata": {
                "confidence": 0.98,
                "taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__OnlyOnce1"]
            }
        },
        {
            "id": "GG_OTU_3",
            "metadata": {
                "confidence": 1.0,
                "taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]
            }
        },
        {
            "id": "GG_OTU_4",
            "metadata": {
                "confidence": 0.842,
                "taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]
            }
        },
        {
            "id": "GG_OTU_5",
            "metadata": {
                "confidence": 1.0,
                "taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__OnlyOnce2"]
            }
        }
    ],
    "shape": [5, 6],
    "type": "OTU table"
}""")
f.close()

from biom import load_table

t = load_table('test.biom')
for e in t.observation_metadata:
    print e['taxonomy']

def collapse_on_family(id_, md): 
    return ';'.join(md['taxonomy'][:6])
t_biom_collapsed = t.collapse(collapse_on_family, axis='observation')

print t_biom_collapsed

!summarize_taxa.py -i test.biom -o summarize_taxa_out/
t_qiime_collapsed = load_table('summarize_taxa_out/test_L6.biom')

print t_qiime_collapsed

collapse_f = lambda id_, md: md['taxonomy'][5]
alt_t_biom_collapsed = t.collapse(collapse_f, axis='observation')
print alt_t_biom_collapsed

collapse_f = lambda id_, md: md['taxonomy'][5]
alt_t_biom_collapsed = t.collapse(collapse_f, axis='observation', min_group_size=1)
print alt_t_biom_collapsed

!print_qiime_config.py