taxa collapsing discrepancy

simple-illustration.ipynb

table.biom

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"s__"]}},{"id": "New.CleanUp.ReferenceOTU12186", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__Roseburia", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12190", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Bifidobacteriales", "f__Bifidobacteriaceae", "g__Bifidobacterium", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12192", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Clostridiaceae", "g__Clostridium", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12198", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12207", "metadata": {"taxonomy": ["k__Bacteria", "p__Verrucomicrobia", "c__Verrucomicrobiae", "o__Verrucomicrobiales", "f__Verrucomicrobiaceae", "g__Akkermansia", "s__muciniphila"]}},{"id": "New.CleanUp.ReferenceOTU12212", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12220", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__[Ruminococcus]", "s__gnavus"]}},{"id": "New.CleanUp.ReferenceOTU12221", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__eggerthii"]}},{"id": "New.CleanUp.ReferenceOTU12224", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Bifidobacteriales", "f__Bifidobacteriaceae", "g__", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12227", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__Dorea", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12238", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__Lachnospira", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12241", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12244", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Erysipelotrichi", "o__Erysipelotrichales", "f__Erysipelotrichaceae", "g__[Eubacterium]", "s__biforme"]}},{"id": "New.CleanUp.ReferenceOTU12252", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Bifidobacteriales", "f__Bifidobacteriaceae", "g__Bifidobacterium", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12266", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae", "g__Faecalibacterium", "s__prausnitzii"]}},{"id": "New.CleanUp.ReferenceOTU12272", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__Dorea", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12273", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12274", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12281", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12284", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12291", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12294", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12295", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae", "g__Faecalibacterium", "s__prausnitzii"]}},{"id": "New.CleanUp.ReferenceOTU12301", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Coriobacteriia", "o__Coriobacteriales", "f__Coriobacteriaceae", "g__Collinsella", "s__stercoris"]}},{"id": "New.CleanUp.ReferenceOTU12307", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae", "g__", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12308", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12310", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Erysipelotrichi", "o__Erysipelotrichales", "f__Erysipelotrichaceae", "g__[Eubacterium]", "s__biforme"]}},{"id": "New.CleanUp.ReferenceOTU12312", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12313", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12322", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12330", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__[Tissierellaceae]", "g__Anaerococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12334", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12341", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12347", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12359", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__Dorea", "s__formicigenerans"]}},{"id": "New.CleanUp.ReferenceOTU12360", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12367", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__[Tissierellaceae]", "g__Anaerococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12368", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae", "g__Faecalibacterium", "s__prausnitzii"]}},{"id": "New.CleanUp.ReferenceOTU12369", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12375", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__[Tissierellaceae]", "g__Anaerococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12386", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12394", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__[Ruminococcus]", "s__gnavus"]}},{"id": "New.CleanUp.ReferenceOTU12395", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12397", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12404", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12409", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12413", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Porphyromonadaceae", "g__Parabacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12421", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12424", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Proteus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12436", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Coriobacteriia", "o__Coriobacteriales", "f__Coriobacteriaceae", "g__Collinsella", "s__stercoris"]}},{"id": "New.CleanUp.ReferenceOTU12440", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12442", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12456", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Aeromonadales", "f__Aeromonadaceae", "g__", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12458", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__[Tissierellaceae]", "g__Anaerococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12461", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Bifidobacteriales", "f__Bifidobacteriaceae", "g__Bifidobacterium", "s__adolescentis"]}},{"id": "New.CleanUp.ReferenceOTU12467", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__luteciae"]}},{"id": "New.CleanUp.ReferenceOTU12468", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12481", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12483", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__[Ruminococcus]", "s__gnavus"]}},{"id": "New.CleanUp.ReferenceOTU12485", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Bifidobacteriales", "f__Bifidobacteriaceae", "g__Bifidobacterium", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12486", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12488", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__[Tissierellaceae]", "g__Anaerococcus", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12490", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", 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"f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12512", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12514", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Coriobacteriia", "o__Coriobacteriales", "f__Coriobacteriaceae", "g__Collinsella", "s__stercoris"]}},{"id": "New.CleanUp.ReferenceOTU12526", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__"]}},{"id": "New.CleanUp.ReferenceOTU12527", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__", "s__"]}}],"columns": [{"id": "MockMiSeq.even", "metadata": null}]}

taxa-collapsing-discrepancy.ipynb

test.biom

{
    "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"
}