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adelq/Input Commands

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Last active August 29, 2015 14:20
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Input Commands
from biom import parse_table
with open('otu_table_hunter.biom') as f:
table = parse_table(f)
print table
table.ids()
table.ids(axis='observation')
table.nnz
normed = table.norm(axis='sample', inplace=False)
phylum_idx = 1
collapse_f = lambda id_, md: "; ".join(md['taxonomy'][:phylum_idx + 1])
collapsed = normed.collapse(collapse_f, axis='observation')
print collapsed
print collapsed
Raw
Output
# Constructed from biom file
#OTU ID 20KHPenn 24KHPenn 26KHPenn 29KHPenn 21KHPenn 19KHPenn 23KHPenn 28KHPenn 25KHPenn 27KHPenn 22KHPenn 18KHPenn
k__Bacteria; p__SBR1093 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Planctomycetes 0.0 1.61967164838e-06 0.0 0.0 0.0 0.0 6.77317234779e-06 0.0 3.68107192815e-07 2.94485754252e-06 3.31296473533e-06 0.0
k__Bacteria; p__AD3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Synergistetes 1.28810648347e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Chlorobi 0.0 0.0 0.0 0.0 1.52392563243e-07 0.0 0.0 1.52392563243e-07 0.0 1.52392563243e-07 0.0 0.0
k__Bacteria; p__OC31 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Proteobacteria 6.6722919902e-05 1.61757973447e-05 1.30384825989e-05 2.33166668163e-05 7.59777739877e-05 6.93620344521e-05 1.67906930817e-05 1.43490632939e-05 1.88642830854e-05 1.75043311999e-05 4.95237924256e-05 7.32668467967e-05
k__Bacteria; p__FBP 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__WS2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__GAL15 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__NC10 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Archaea; p__[Parvarchaeota] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__BRC1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__OP9 4.86144871172e-07 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.21536217793e-07 0.0 0.0
k__Bacteria; p__OP8 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Acidobacteria 2.33957219251e-07 0.0 3.3422459893e-07 0.0 3.3422459893e-08 0.0 0.0 3.3422459893e-08 5.01336898396e-07 5.34759358289e-07 6.68449197861e-08 0.0
k__Bacteria; p__Nitrospirae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__OP3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Gemmatimonadetes 0.0 0.0 0.0 1.20196685485e-05 0.0 0.0 0.0 0.0 1.82116190129e-06 1.91221999636e-05 0.0 0.0
k__Bacteria; p__OP1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__OD1 0.0 7.08717221828e-07 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Thermotogae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__SR1 3.52941176471e-05 0.000164705882353 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__NKB19 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Armatimonadetes 0.0 1.48116800677e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Tenericutes 0.0 1.6693163752e-05 0.0 0.0 0.0 0.0 0.0 2.38473767886e-05 0.0 0.0 0.0 0.0
k__Bacteria; p__TPD-58 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__KSB3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__TM6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__ 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Verrucomicrobia 0.0 1.15089514066e-06 0.0 0.0 0.0 0.0 0.0 3.19693094629e-06 0.0 0.0 0.0 0.0
k__Bacteria; p__Spirochaetes 0.0 1.80203372377e-06 1.28716694555e-07 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.28716694555e-07
k__Bacteria; p__TM7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__LD1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__PAUC34f 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Bacteroidetes 1.44809110562e-07 7.1783944807e-06 3.7753803825e-06 5.16141044074e-06 4.13740315891e-08 1.03435078973e-08 6.44400542e-06 1.86390012309e-05 1.06434696263e-05 5.73030337509e-06 1.33741557112e-05 2.06870157945e-08
k__Bacteria; p__Kazan-3B-28 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Chloroflexi 8.65370053869e-08 2.48793890487e-07 1.48194621725e-06 1.52521471994e-06 1.08171256734e-08 0.0 3.24513770201e-07 1.40622633754e-07 6.92296043095e-07 2.40140189949e-06 2.16342513467e-07 1.08171256734e-08
k__Bacteria; p__GOUTA4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__OP11 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.61764705882e-06 0.0 0.0 0.0
k__Archaea; p__Euryarchaeota 3.65887981987e-06 0.0 0.0 0.0 0.0 0.0 1.60427807487e-05 0.0 1.94202082747e-05 1.12580917534e-06 0.0 0.0
k__Bacteria; p__WWE1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__WS4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__WS5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__[Thermi] 1.34453781513e-05 5.04201680672e-05 8.40336134454e-06 6.38655462185e-05 0.0 0.0 0.0 0.0 7.2268907563e-05 0.0 1.00840336134e-05 0.0
k__Bacteria; p__AC1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__WS3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__ZB3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Cyanobacteria 1.99240986717e-05 0.000342979127135 0.00036669829222 0.000319734345351 0.0 0.0 0.00010009487666 0.000106736242884 0.000119070208729 0.000468216318786 7.68500948767e-05 0.0
k__Bacteria; p__H-178 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__WS1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__SC4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Elusimicrobia 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Fusobacteria 0.0 0.00138725490196 1.30718954248e-05 0.000467320261438 0.0 0.0 0.000718954248366 0.000957516339869 0.000459150326797 0.000607843137255 0.0 0.0
k__Bacteria; p__GN04 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Fibrobacteres 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__GN02 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.000328431372549 0.0 0.0 0.0 0.0
k__Bacteria; p__Lentisphaerae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__MAT-CR-M4-B07 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__LCP-89 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Actinobacteria 4.20369586684e-06 0.000112399492171 0.000143687403019 0.000104358865848 6.20679926647e-07 3.38552687262e-07 0.000121173649316 8.73748060375e-05 7.12371279447e-05 0.00011747778248 3.55198194386e-05 2.25701791508e-07
k__Bacteria; p__[Caldithrix] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Chlamydiae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.92041522491e-06 0.0 0.0
k__Bacteria; p__Poribacteria 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Unassigned 0.0 0.0 0.0 4.95703899537e-07 1.65234633179e-08 0.0 3.30469266358e-08 7.1050892267e-07 1.65234633179e-08 8.26173165896e-08 1.65234633179e-08 1.65234633179e-08
k__Bacteria; p__Firmicutes 2.24948630955e-05 8.35284560615e-05 9.20222678836e-05 7.61217565824e-05 5.01744158264e-07 1.83136617767e-05 8.9704687724e-05 9.45309886749e-05 0.000101483729154 7.90485975056e-05 3.79653079753e-05 7.92038992689e-06
k__Bacteria; p__Caldiserica 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__WPS-2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__FCPU426 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Archaea; p__Crenarchaeota 0.0 7.8431372549e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__Hyd24-12 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria; p__SAR406 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
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