Merge pull request #6 from borenstein-lab/count_feature_tables

Added taxonomy tables with read counts

.gitignore

@@ -18,6 +18,7 @@ data/prelim_data
 data/processed_data/iHMP_IBDMDB_2019/mtb.tsv
 data/processed_data/YACHIDA_CRC_2019/species.tsv
 data/processed_data_V1
+data/processed_data_V2
 
 # Reference DB files
 references/gtdb/bac120_metadata_r202.tsv
@@ -29,9 +30,6 @@ docs/~$*.xlsx
 scripts/.RData
 
 scripts/data_analysis/iPATH_selection.txt
-scripts/data_analysis/GLay_clusters_3.png
-scripts/data_analysis/GLay_clusters.png
-scripts/data_analysis/GLay_clusters_2.png
 scripts/data_analysis/cytoscape_visualization.cys
 scripts/data_organization/utils_old.R
 scripts/data_analysis/.RData

data/processed_data/HE_INFANTS_MFGM_2019/mtb.map.tsv

@@ -6,12 +6,12 @@ Compound	High.Confidence.Annotation	HMDB	KEGG
 2-Aminobutyrate	TRUE	HMDB0000452	C02356
 2-Hydroxybutyrate	TRUE	HMDB0000008	C05984
 2-Hydroxyglutarate	TRUE	HMDB0059655	C02630
-2-Hydroxyisobutyrate	TRUE	HMDB0000729	C21297
+2-Hydroxyisobutyrate	TRUE	HMDB0242161	C21297
 2-Hydroxyisovalerate	TRUE	HMDB0000407	NA
 2-Oxoglutarate	TRUE	HMDB0000208	C00026
 3'-sialyllactose	TRUE	HMDB0000825	NA
 3' fucosyl lactose	TRUE	HMDB0002094	NA
-3-Hydroxybutyrate	TRUE	HMDB0000357	C01089
+3-Hydroxybutyrate	TRUE	HMDB0000011	C01089
 3-Phenyllactate	TRUE	HMDB0000779	C01479
 4-Aminobutyrate	TRUE	HMDB0000112	C00334
 4-Hydroxybenzoate	TRUE	HMDB0000500	C00156
@@ -23,19 +23,19 @@ Compound	High.Confidence.Annotation	HMDB	KEGG
 Acetaminophen	TRUE	HMDB0001859	C06804
 Acetate	TRUE	HMDB0000042	C00033
 Acetoin	TRUE	HMDB0003243	C00466
-Alanine	TRUE	HMDB0000161	C00041
+Alanine	TRUE	HMDB0000161	C01401
 Allantoin	TRUE	HMDB0000462	C01551
-Arabinose	TRUE	HMDB0000646	C02479
+Arabinose	TRUE	HMDB0000646	C00259
 Arginine	TRUE	HMDB0000517	C00062
-Ascorbate	TRUE	NA	C00072
+Ascorbate	TRUE	HMDB0000044	C00072
 Asparagine	TRUE	HMDB0000168	C00152
 Aspartate	TRUE	HMDB0000191	C00049
 beta-Alanine	TRUE	HMDB0000056	C00099
 beta-Pseudouridine	TRUE	HMDB0000767	C02067
 Betaine	TRUE	HMDB0000043	C00719
 Butyrate	TRUE	HMDB0000039	C00246
 Cadaverine	TRUE	HMDB0002322	C01672
-Carnitine	TRUE	HMDB0000062	C00318
+Carnitine	TRUE	HMDB0000062	C00487
 Choline	TRUE	HMDB0000097	C00114
 Citrate	TRUE	HMDB0000094	C00158
 Citrulline	TRUE	HMDB0000904	C00327
@@ -49,12 +49,12 @@ DL-methionine-sulfoxide	TRUE	NA	C02989
 Ethanol	TRUE	HMDB0000108	C00469
 Ethanolamine	TRUE	HMDB0000149	C00189
 Ethyl-beta-D-glucuronide	TRUE	HMDB0010325	NA
-Formate	TRUE	HMDB0000142	C00058
-Fucose	TRUE	HMDB0012327	C02781
+Formate	TRUE	HMDB0304356	NA
+Fucose	TRUE	HMDB0000174	C01019
 Fumarate	TRUE	HMDB0000134	C00122
-Galactose	TRUE	HMDB0000143	C00984
-Glucose	TRUE	HMDB0000122	C00221
-Glutamate	TRUE	HMDB0000148	C00025
+Galactose	TRUE	HMDB0000143	C00124
+Glucose	TRUE	HMDB0000122	C00031
+Glutamate	TRUE	HMDB0000148	C00302
 Glutamine	TRUE	HMDB0000641	C00064
 Glutarate	TRUE	HMDB0000661	C00489
 Glycerol	TRUE	HMDB0000131	C00116
@@ -73,7 +73,7 @@ Lactate	TRUE	HMDB0000190	C00186
 Lacto-N-fucopentaose I	TRUE	HMDB0006705	NA
 Lacto-N-fucopentaose III	TRUE	HMDB0006576	NA
 Lactodifucotetraose	TRUE	HMDB0006587	NA
-Lactose	TRUE	HMDB0041627	C01970
+Lactose	TRUE	HMDB0000186	C00243
 Leucine	TRUE	HMDB0000687	C00123
 Lysine	TRUE	HMDB0000182	C00047
 Malate	TRUE	HMDB0000156	C00149
@@ -91,18 +91,18 @@ Nicotinate	TRUE	HMDB0001488	C00253
 O-Acetylcarnitine	TRUE	HMDB0000201	C02571
 Ornithine	TRUE	HMDB0000214	C00077
 p-Cresol	TRUE	HMDB0001858	C01468
-Phenol	TRUE	HMDB0000228	C15584
+Phenol	TRUE	HMDB0000228	C00146
 Phenylacetate	TRUE	HMDB0000209	C07086
 Phenylalanine	TRUE	HMDB0000159	C00079
 Proline	TRUE	HMDB0000162	C00148
 Propionate	TRUE	HMDB0000237	C00163
-Propylene glycol	TRUE	HMDB0001881	C02912
+Propylene glycol	TRUE	HMDB0001881	C00583
 Putrescine	TRUE	HMDB0001414	C00134
 Pyroglutamate	TRUE	HMDB0000267	C01879
 Pyruvate	TRUE	HMDB0000243	C00022
 Ribose	TRUE	HMDB0000283	C00121
 Sarcosine	TRUE	HMDB0000271	C00213
-Serine	TRUE	HMDB0000187	C00716
+Serine	TRUE	HMDB0000187	C00065
 Succinate	TRUE	HMDB0000254	C00042
 Taurine	TRUE	HMDB0000251	C00245
 Threonine	TRUE	HMDB0000167	C00188

data/processed_data/KANG_AUTISM_2017/mtb.map.tsv

@@ -1,10 +1,10 @@
 Compound	HMDB	KEGG	High.Confidence.Annotation
 2-Aminobutyrate	HMDB0000452	C02356	TRUE
-2-Hydroxyisobutyrate	HMDB0000729	NA	TRUE
+2-Hydroxyisobutyrate	HMDB0242161	NA	TRUE
 3-Phenylpropionate	HMDB0000764	C05629	TRUE
 4-Aminobutyrate	HMDB0000112	C00334	TRUE
 Acetate	HMDB0000042	C00033	TRUE
-Alanine	HMDB0000161	C00041	TRUE
+Alanine	HMDB0000161	C01401	TRUE
 Arginine	HMDB0000517	C00062	TRUE
 Asparagine	HMDB0000168	C00152	TRUE
 Aspartate	HMDB0000191	C00049	TRUE
@@ -14,10 +14,10 @@ Caprate	HMDB0000511	C01571	TRUE
 Choline	HMDB0000097	C00114	TRUE
 DSS-d6 (Chemical Shape Indicator)	NA	NA	TRUE
 Ethanol	HMDB0000108	C00469	TRUE
-Formate	HMDB0000142	C00058	TRUE
+Formate	HMDB0304356	C00058	TRUE
 Fumarate	HMDB0000134	C00122	TRUE
-Glucose	HMDB0000122	C00221	TRUE
-Glutamate	HMDB0000148	C00025	TRUE
+Glucose	HMDB0000122	C00031	TRUE
+Glutamate	HMDB0000148	C00302	TRUE
 Glutamine	HMDB0000641	C00064	TRUE
 Glycerol	HMDB0000131	C00116	TRUE
 Glycine	HMDB0000123	C00037	TRUE
@@ -30,7 +30,7 @@ Isovalerate	HMDB0000718	C08262	TRUE
 Lactate	HMDB0000190	C00186	TRUE
 Leucine	HMDB0000687	C00123	TRUE
 Lysine	HMDB0000182	C00047	TRUE
-Malonate	NA	C00383	TRUE
+Malonate	HMDB0000691	C00383	TRUE
 Methanol	HMDB0001875	C00132	TRUE
 Methionine	HMDB0000696	C00073	TRUE
 Methylamine	HMDB0000164	C00218	TRUE
@@ -46,7 +46,7 @@ Phenylalanine	HMDB0000159	C00079	TRUE
 Proline	HMDB0000162	C00148	TRUE
 Propionate	HMDB0000237	C00163	TRUE
 Pyruvate	HMDB0000243	C00022	TRUE
-Serine	HMDB0000187	C00716	TRUE
+Serine	HMDB0000187	C00065	TRUE
 Succinate	HMDB0000254	C00042	TRUE
 Taurine	HMDB0000251	C00245	TRUE
 Threonine	HMDB0000167	C00188	TRUE