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added output corresponding to new interface

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1 parent 6094071 commit 5be1b75a624401bcd1ea47fde903b430c923da4d @gregcaporaso gregcaporaso committed Jun 14, 2012
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  1. BIN compute_core_microbiome/otu_table_core/core_otu_size.pdf
  2. +2 −0 compute_core_microbiome/otu_table_core/core_otus_100.txt
  3. +12 −0 compute_core_microbiome/otu_table_core/core_otus_50.txt
  4. +12 −0 compute_core_microbiome/otu_table_core/core_otus_55.txt
  5. +9 −0 compute_core_microbiome/otu_table_core/core_otus_60.txt
  6. +9 −0 compute_core_microbiome/otu_table_core/core_otus_65.txt
  7. +4 −0 compute_core_microbiome/otu_table_core/core_otus_70.txt
  8. +4 −0 compute_core_microbiome/otu_table_core/core_otus_75.txt
  9. +2 −0 compute_core_microbiome/otu_table_core/core_otus_80.txt
  10. +2 −0 compute_core_microbiome/otu_table_core/core_otus_85.txt
  11. +2 −0 compute_core_microbiome/otu_table_core/core_otus_90.txt
  12. +2 −0 compute_core_microbiome/otu_table_core/core_otus_95.txt
  13. +1 −0 compute_core_microbiome/otu_table_core/core_table_100.biom
  14. +1 −0 compute_core_microbiome/otu_table_core/core_table_50.biom
  15. +1 −0 compute_core_microbiome/otu_table_core/core_table_55.biom
  16. +1 −0 compute_core_microbiome/otu_table_core/core_table_60.biom
  17. +1 −0 compute_core_microbiome/otu_table_core/core_table_65.biom
  18. +1 −0 compute_core_microbiome/otu_table_core/core_table_70.biom
  19. +1 −0 compute_core_microbiome/otu_table_core/core_table_75.biom
  20. +1 −0 compute_core_microbiome/otu_table_core/core_table_80.biom
  21. +1 −0 compute_core_microbiome/otu_table_core/core_table_85.biom
  22. +1 −0 compute_core_microbiome/otu_table_core/core_table_90.biom
  23. +1 −0 compute_core_microbiome/otu_table_core/core_table_95.biom
  24. BIN compute_core_microbiome/otu_table_core_fast/core_otu_size.pdf
  25. +7 −0 compute_core_microbiome/otu_table_core_fast/core_otus_100.txt
  26. +42 −0 compute_core_microbiome/otu_table_core_fast/core_otus_50.txt
  27. +19 −0 compute_core_microbiome/otu_table_core_fast/core_otus_55.txt
  28. +19 −0 compute_core_microbiome/otu_table_core_fast/core_otus_60.txt
  29. +19 −0 compute_core_microbiome/otu_table_core_fast/core_otus_65.txt
  30. +19 −0 compute_core_microbiome/otu_table_core_fast/core_otus_70.txt
  31. +19 −0 compute_core_microbiome/otu_table_core_fast/core_otus_75.txt
  32. +7 −0 compute_core_microbiome/otu_table_core_fast/core_otus_80.txt
  33. +7 −0 compute_core_microbiome/otu_table_core_fast/core_otus_85.txt
  34. +7 −0 compute_core_microbiome/otu_table_core_fast/core_otus_90.txt
  35. +7 −0 compute_core_microbiome/otu_table_core_fast/core_otus_95.txt
  36. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_100.biom
  37. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_50.biom
  38. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_55.biom
  39. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_60.biom
  40. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_65.biom
  41. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_70.biom
  42. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_75.biom
  43. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_80.biom
  44. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_85.biom
  45. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_90.biom
  46. +1 −0 compute_core_microbiome/otu_table_core_fast/core_table_95.biom
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BIN compute_core_microbiome/otu_table_core/core_otu_size.pdf
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2 compute_core_microbiome/otu_table_core/core_otus_100.txt
@@ -0,0 +1,2 @@
+# Core OTUs across 100 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
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12 compute_core_microbiome/otu_table_core/core_otus_50.txt
@@ -0,0 +1,12 @@
+# Core OTUs across 50 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+70 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+275 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+319 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+396 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
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12 compute_core_microbiome/otu_table_core/core_otus_55.txt
@@ -0,0 +1,12 @@
+# Core OTUs across 55 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+70 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+275 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+319 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+396 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
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9 compute_core_microbiome/otu_table_core/core_otus_60.txt
@@ -0,0 +1,9 @@
+# Core OTUs across 60 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+70 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+396 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
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9 compute_core_microbiome/otu_table_core/core_otus_65.txt
@@ -0,0 +1,9 @@
+# Core OTUs across 65 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+70 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+396 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
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4 compute_core_microbiome/otu_table_core/core_otus_70.txt
@@ -0,0 +1,4 @@
+# Core OTUs across 70 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+70 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
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4 compute_core_microbiome/otu_table_core/core_otus_75.txt
@@ -0,0 +1,4 @@
+# Core OTUs across 75 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+70 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
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2 compute_core_microbiome/otu_table_core/core_otus_80.txt
@@ -0,0 +1,2 @@
+# Core OTUs across 80 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
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2 compute_core_microbiome/otu_table_core/core_otus_85.txt
@@ -0,0 +1,2 @@
+# Core OTUs across 85 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
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2 compute_core_microbiome/otu_table_core/core_otus_90.txt
@@ -0,0 +1,2 @@
+# Core OTUs across 90 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
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2 compute_core_microbiome/otu_table_core/core_otus_95.txt
@@ -0,0 +1,2 @@
+# Core OTUs across 95 % of samples.
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
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1 compute_core_microbiome/otu_table_core/core_table_100.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [1, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.808373", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_50.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "70", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "73", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "92", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "275", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "319", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "371", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "378", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "396", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "399", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5], [2, 1, 10, 2, 24, 0, 0, 1, 1], [0, 0, 0, 0, 2, 2, 1, 4, 1], [0, 4, 4, 0, 1, 2, 0, 2, 1], [1, 5, 3, 2, 0, 0, 0, 0, 1], [11, 12, 5, 13, 2, 0, 0, 0, 0], [0, 2, 2, 4, 0, 5, 1, 5, 0], [2, 18, 0, 1, 0, 0, 21, 4, 4], [0, 1, 2, 0, 9, 1, 1, 1, 3], [0, 2, 3, 1, 4, 0, 5, 0, 4], [0, 2, 1, 2, 0, 0, 1, 1, 1]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [11, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.574406", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_55.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "70", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "73", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "92", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "275", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "319", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "371", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "378", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "396", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "399", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5], [2, 1, 10, 2, 24, 0, 0, 1, 1], [0, 0, 0, 0, 2, 2, 1, 4, 1], [0, 4, 4, 0, 1, 2, 0, 2, 1], [1, 5, 3, 2, 0, 0, 0, 0, 1], [11, 12, 5, 13, 2, 0, 0, 0, 0], [0, 2, 2, 4, 0, 5, 1, 5, 0], [2, 18, 0, 1, 0, 0, 21, 4, 4], [0, 1, 2, 0, 9, 1, 1, 1, 3], [0, 2, 3, 1, 4, 0, 5, 0, 4], [0, 2, 1, 2, 0, 0, 1, 1, 1]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [11, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.597645", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_60.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "70", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "92", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "371", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "378", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "396", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "399", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5], [2, 1, 10, 2, 24, 0, 0, 1, 1], [0, 4, 4, 0, 1, 2, 0, 2, 1], [0, 2, 2, 4, 0, 5, 1, 5, 0], [2, 18, 0, 1, 0, 0, 21, 4, 4], [0, 1, 2, 0, 9, 1, 1, 1, 3], [0, 2, 3, 1, 4, 0, 5, 0, 4], [0, 2, 1, 2, 0, 0, 1, 1, 1]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [8, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.620528", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_65.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "70", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "92", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "371", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "378", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "396", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "399", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5], [2, 1, 10, 2, 24, 0, 0, 1, 1], [0, 4, 4, 0, 1, 2, 0, 2, 1], [0, 2, 2, 4, 0, 5, 1, 5, 0], [2, 18, 0, 1, 0, 0, 21, 4, 4], [0, 1, 2, 0, 9, 1, 1, 1, 3], [0, 2, 3, 1, 4, 0, 5, 0, 4], [0, 2, 1, 2, 0, 0, 1, 1, 1]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [8, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.642708", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_70.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "70", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5], [2, 1, 10, 2, 24, 0, 0, 1, 1], [0, 1, 2, 0, 9, 1, 1, 1, 3]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [3, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.665754", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_75.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "70", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5], [2, 1, 10, 2, 24, 0, 0, 1, 1], [0, 1, 2, 0, 9, 1, 1, 1, 3]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [3, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.689409", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_80.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [1, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.712526", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_85.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [1, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.738129", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_90.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [1, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.761069", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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1 compute_core_microbiome/otu_table_core/core_table_95.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[1, 3, 1, 2, 1, 9, 2, 4, 5]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [1, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:50:56.784185", "type": "OTU table", "id": null, "matrix_element_type": "int"}
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BIN compute_core_microbiome/otu_table_core_fast/core_otu_size.pdf
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7 compute_core_microbiome/otu_table_core_fast/core_otus_100.txt
@@ -0,0 +1,7 @@
+# Core OTUs across 100 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
42 compute_core_microbiome/otu_table_core_fast/core_otus_50.txt
@@ -0,0 +1,42 @@
+# Core OTUs across 50 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+0 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+8 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+59 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+70 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+74 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+75 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+78 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+84 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+89 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Porphyromonadaceae']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+102 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Porphyromonadaceae']
+153 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+161 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+164 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+175 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+180 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+187 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+214 [u'Root', u'k__Bacteria']
+247 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+250 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+252 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+267 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+278 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+286 [u'Root', u'k__Bacteria', u'p__Proteobacteria', u'c__Deltaproteobacteria', u'o__Desulfovibrionales', u'f__Desulfovibrionaceae']
+304 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+321 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+347 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+349 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+359 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Clostridiales Family XIII. Incertae Sedis']
+368 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+396 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+412 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
19 compute_core_microbiome/otu_table_core_fast/core_otus_55.txt
@@ -0,0 +1,19 @@
+# Core OTUs across 55 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+59 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+74 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+84 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+153 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+187 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+247 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+321 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+412 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
19 compute_core_microbiome/otu_table_core_fast/core_otus_60.txt
@@ -0,0 +1,19 @@
+# Core OTUs across 60 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+59 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+74 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+84 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+153 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+187 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+247 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+321 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+412 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
19 compute_core_microbiome/otu_table_core_fast/core_otus_65.txt
@@ -0,0 +1,19 @@
+# Core OTUs across 65 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+59 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+74 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+84 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+153 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+187 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+247 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+321 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+412 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
19 compute_core_microbiome/otu_table_core_fast/core_otus_70.txt
@@ -0,0 +1,19 @@
+# Core OTUs across 70 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+59 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+74 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+84 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+153 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+187 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+247 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+321 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+412 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
19 compute_core_microbiome/otu_table_core_fast/core_otus_75.txt
@@ -0,0 +1,19 @@
+# Core OTUs across 75 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+59 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+74 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+84 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+92 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+153 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+187 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Ruminococcaceae']
+247 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+321 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+371 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+378 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Bacteroidaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+399 [u'Root', u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia', u'o__Clostridiales', u'f__Lachnospiraceae']
+412 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
7 compute_core_microbiome/otu_table_core_fast/core_otus_80.txt
@@ -0,0 +1,7 @@
+# Core OTUs across 80 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
7 compute_core_microbiome/otu_table_core_fast/core_otus_85.txt
@@ -0,0 +1,7 @@
+# Core OTUs across 85 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
7 compute_core_microbiome/otu_table_core_fast/core_otus_90.txt
@@ -0,0 +1,7 @@
+# Core OTUs across 90 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
7 compute_core_microbiome/otu_table_core_fast/core_otus_95.txt
@@ -0,0 +1,7 @@
+# Core OTUs across 95 % of samples matching the sample metadata pattern "Treatment:Fast":
+# PC.607 PC.634 PC.635 PC.636
+49 [u'Root', u'k__Bacteria', u'p__Deferribacteres', u'c__Deferribacteres', u'o__Deferribacterales', u'f__Deferribacteraceae']
+63 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+73 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
+377 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__Rikenellaceae']
+394 [u'Root', u'k__Bacteria', u'p__Bacteroidetes', u'c__Bacteroidia', u'o__Bacteroidales', u'f__']
View
1 compute_core_microbiome/otu_table_core_fast/core_table_100.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "49", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Deferribacteres", "c__Deferribacteres", "o__Deferribacterales", "f__Deferribacteraceae"]}}, {"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "73", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "377", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[0, 0, 0, 0, 0, 3, 5, 2, 6], [1, 3, 1, 2, 1, 9, 2, 4, 5], [0, 0, 0, 0, 2, 2, 1, 4, 1], [0, 0, 0, 0, 0, 5, 9, 5, 3], [0, 1, 2, 0, 9, 1, 1, 1, 3]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [5, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:51:04.862852", "type": "OTU table", "id": null, "matrix_element_type": "int"}
View
1 compute_core_microbiome/otu_table_core_fast/core_table_50.biom
@@ -0,0 +1 @@
+{"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "8", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "49", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Deferribacteres", "c__Deferribacteres", "o__Deferribacterales", "f__Deferribacteraceae"]}}, {"id": "59", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "63", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "70", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "73", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "74", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "75", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "78", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "84", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "89", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Porphyromonadaceae"]}}, {"id": "92", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "102", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Porphyromonadaceae"]}}, {"id": "153", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "161", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "164", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "175", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "180", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "187", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "214", "metadata": {"taxonomy": ["Root", "k__Bacteria"]}}, {"id": "247", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "250", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "252", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "267", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "278", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "286", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Proteobacteria", "c__Deltaproteobacteria", "o__Desulfovibrionales", "f__Desulfovibrionaceae"]}}, {"id": "304", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "321", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "347", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "349", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "359", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Clostridiales Family XIII. Incertae Sedis"]}}, {"id": "368", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "371", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "377", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Rikenellaceae"]}}, {"id": "378", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "396", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "399", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "412", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}], "format": "Biological Observation Matrix 0.9.3", "data": [[0, 0, 0, 0, 0, 0, 2, 1, 0], [1, 0, 1, 0, 0, 0, 0, 1, 1], [0, 0, 0, 0, 0, 3, 5, 2, 6], [0, 0, 0, 1, 0, 0, 4, 10, 37], [1, 3, 1, 2, 1, 9, 2, 4, 5], [2, 1, 10, 2, 24, 0, 0, 1, 1], [0, 0, 0, 0, 2, 2, 1, 4, 1], [0, 0, 0, 0, 0, 0, 2, 3, 2], [0, 0, 2, 0, 0, 0, 0, 1, 2], [0, 0, 0, 0, 0, 0, 0, 2, 2], [0, 0, 0, 1, 0, 0, 1, 2, 19], [0, 0, 0, 0, 0, 0, 1, 3, 0], [0, 4, 4, 0, 1, 2, 0, 2, 1], [0, 0, 0, 1, 0, 0, 3, 1, 0], [0, 0, 0, 1, 0, 0, 1, 5, 2], [0, 0, 0, 0, 0, 0, 0, 1, 1], [0, 0, 0, 0, 0, 0, 0, 1, 1], [0, 0, 0, 0, 0, 0, 1, 0, 1], [0, 0, 1, 0, 0, 2, 0, 1, 0], [0, 0, 0, 1, 0, 1, 0, 1, 1], [0, 0, 0, 0, 0, 2, 0, 1, 0], [0, 0, 0, 0, 0, 7, 0, 2, 2], [0, 0, 0, 0, 0, 1, 0, 1, 0], [0, 0, 0, 0, 0, 1, 1, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 1], [0, 0, 0, 0, 0, 6, 0, 3, 0], [0, 0, 0, 0, 0, 0, 2, 0, 1], [0, 0, 0, 0, 0, 1, 0, 1, 0], [0, 0, 0, 0, 0, 0, 1, 1, 1], [1, 0, 0, 0, 2, 0, 2, 0, 3], [0, 0, 0, 0, 0, 0, 2, 1, 0], [0, 0, 0, 0, 0, 1, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 1], [0, 2, 2, 4, 0, 5, 1, 5, 0], [0, 0, 0, 0, 0, 5, 9, 5, 3], [2, 18, 0, 1, 0, 0, 21, 4, 4], [0, 1, 2, 0, 9, 1, 1, 1, 3], [0, 2, 3, 1, 4, 0, 5, 0, 4], [0, 2, 1, 2, 0, 0, 1, 1, 1], [0, 0, 0, 0, 0, 0, 8, 10, 2]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.5.0-dev, svn revision 3069", "matrix_type": "dense", "shape": [40, 9], "format_url": "http://biom-format.org", "date": "2012-06-14T17:51:04.627855", "type": "OTU table", "id": null, "matrix_element_type": "int"}
View
1 compute_core_microbiome/otu_table_core_fast/core_table_55.biom
@@ -0,0 +1 @@
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1 compute_core_microbiome/otu_table_core_fast/core_table_60.biom
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1 compute_core_microbiome/otu_table_core_fast/core_table_65.biom
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1 compute_core_microbiome/otu_table_core_fast/core_table_70.biom
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1 compute_core_microbiome/otu_table_core_fast/core_table_75.biom
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1 compute_core_microbiome/otu_table_core_fast/core_table_80.biom
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1 compute_core_microbiome/otu_table_core_fast/core_table_85.biom
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1 compute_core_microbiome/otu_table_core_fast/core_table_90.biom
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1 compute_core_microbiome/otu_table_core_fast/core_table_95.biom
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