Mercurial > repos > czouaoui > abundance_table_to_biom1
changeset 0:5ac3be5b1d12 draft
Uploaded
| author | czouaoui |
|---|---|
| date | Tue, 20 Mar 2018 04:21:57 -0400 |
| parents | |
| children | 10eedb4b587f |
| files | abundanceTable_to_biom/abundanceTable_to_biom.py abundanceTable_to_biom/abundanceTable_to_biom.py~ abundanceTable_to_biom/abundanceTable_to_biom.xml abundanceTable_to_biom/abundanceTable_to_biom.xml~ abundanceTable_to_biom/test-data/biom_result.biom abundanceTable_to_biom/test-data/merge_summary_reads.csv |
| diffstat | 6 files changed, 275 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundanceTable_to_biom/abundanceTable_to_biom.py Tue Mar 20 04:21:57 2018 -0400 @@ -0,0 +1,66 @@ +import datetime +import argparse +import csv +import json + +def __main__(): + print "Generating biom file ..." + options = argsParser() + families, samples, data = abundanceTableParser(options.file) + biom_file = constructBiom(families, samples, data) + file_name = options.out_name + '.biom' if options.out_name else 'result.biom' + with open(file_name, 'w') as output: + json.dump(biom_file, output) + print "Your biom file (" + file_name + ") is now created" + +def argsParser(): + parser = argparse.ArgumentParser() + parser.add_argument("-f", "--file", type=argparse.FileType('r'), help="Abundance table in csv format") + parser.add_argument("-o", "--out_name", help="BIOM (v1.0) file name") + + return parser.parse_args() + +def abundanceTableParser(file): + with file: + reader = csv.reader(file) + + families = [] + for i, row in enumerate(reader): + if i != 0: + families.append({"id":"OTU_" + str(i), "metadata":{"taxonomy":["k__", "p__", "c__", "o__", + "f__" + row[0], "g__", "s__"]}}) + + file.seek(0) + first_row = next(reader) + samples = [] + for i in range(1, len(first_row)): + samples.append({"id":first_row[i], "metadata":{"phinchID":first_row[i]}}) + + file.seek(0) + data = [] + for i, row in enumerate(reader): + if i != 0: + for j in range(1, len(row)): + if row[j] != 'NA': + data.append([i - 1, j - 1, int(row[j])]) + + return families, samples, data + +def constructBiom(families, samples, data): + biom = {"id":"null", + "format": "Biological Observation Matrix 0.9.1-dev", + "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html", + "type": "OTU table", + "generated_by": "abundanceTable_to_biom script", + "date": datetime.date.today().isoformat(), + "matrix_type": "sparse", + "matrix_element_type": "int", + "shape": [len(families), len(samples)], + "rows":families, + "columns":samples, + "data":data} + return biom + + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundanceTable_to_biom/abundanceTable_to_biom.py~ Tue Mar 20 04:21:57 2018 -0400 @@ -0,0 +1,66 @@ +import datetime +import argparse +import csv +import json + +def __main__(): + print "Generating biom file ..." + options = argsParser() + families, samples, data = abundanceTableParser(options.file) + biom_file = constructBiom(families, samples, data) + file_name = options.out_name + '.biom' if options.out_name else 'result.biom' + with open(file_name, 'w') as output: + json.dump(biom_file, output) + print "Your biom file (" + file_name + ") is now created" + +def argsParser(): + parser = argparse.ArgumentParser() + parser.add_argument("-f", "--file", type=argparse.FileType('r'), help="Abundance table in csv format") + parser.add_argument("-o", "--out_name", help="BIOM (v1.0) file name") + + return parser.parse_args() + +def abundanceTableParser(file): + with file: + reader = csv.reader(file) + + families = [] + for i, row in enumerate(reader): + if i != 0: + families.append({"id":"OTU_" + str(i), "metadata":{"taxonomy":["k__", "p__", "c__", "o__", + "f__" + row[0], "g__", "s__"]}}) + + file.seek(0) + first_row = next(reader) + samples = [] + for i in range(1, len(first_row)): + samples.append({"id":first_row[i], "metadata":{"phinchID":first_row[i]}}) + + file.seek(0) + data = [] + for i, row in enumerate(reader): + if i != 0: + for j in range(1, len(row)): + if row[j] != 'NA': + data.append([i - 1, j - 1, int(row[j])]) + + return families, samples, data + +def constructBiom(families, samples, data): + biom = {"id":"null", + "format": "Biological Observation Matrix 0.9.1-dev", + "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html", + "type": "OTU table", + "generated_by": "abundanceTable_to_biom script", + "date": datetime.date.today().isoformat(), + "matrix_type": "sparse", + "matrix_element_type": "int", + "shape": [len(families), len(samples)], + "rows":families, + "columns":samples, + "data":data} + return biom + + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundanceTable_to_biom/abundanceTable_to_biom.xml Tue Mar 20 04:21:57 2018 -0400 @@ -0,0 +1,22 @@ +<tool id="abundanceTable_to_biom" name="Converting abundance tables to Biom files (v1.0)" version="0.1.0"> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/abundanceTable_to_biom.py --file $input --out_name biom_result + ]]></command> + <inputs> + <param type="data" name="input" format="csv" label="Abundance table"/> + </inputs> + <outputs> + <data name= "output" format="biom" label="${input.name} to Biom (v1.0)" from_work_dir="biom_result.biom"/> + </outputs> + <tests> + <test> + <param name="input" format="csv" value="merge_summary_reads.csv"/> + <output name="output" format="biom" file="biom_result.biom"/> + </test> + </tests> + <help><![CDATA[ + This tool is used to generate a Biom file (v1.0) from an abundance table. + The first column of the header is a taxonomy list (families). Next columns contain sample ids. + The abundancy of reads is set inside the table. + ]]></help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundanceTable_to_biom/abundanceTable_to_biom.xml~ Tue Mar 20 04:21:57 2018 -0400 @@ -0,0 +1,22 @@ +<tool id="abundanceTable_to_biom" name="Converting abundance tables to Biom files (v1.0)" version="0.1.0"> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/abundanceTable_to_biom.py --file $input --out_name biom_result + ]]></command> + <inputs> + <param type="data" name="input" format="csv" label="Abundance table"/> + </inputs> + <outputs> + <data name= "output" format="biom" label="${input.name} to Biom (v1.0)" from_work_dir="biom_result.biom"/> + </outputs> + <tests> + <test> + <param name="input" format="csv" value="merge_summary_reads.csv"/> + <output name="output" format="biom" file="biom_result.biom"/> + </test> + </tests> + <help><![CDATA[ + This tool is used to generate a Biom file (v1.0) from an abundance table. + The first column of the header is a taxonomy list (families). Next columns contain sample ids. + The abundancy of reads is set inside the table. + ]]></help> +</tool>
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Incertae Sedis", "g__", "s__"]}}, {"id": "OTU_92", "metadata": {"taxonomy": ["k__", "p__", "c__", "o__", "f__Desulfobulbaceae", "g__", "s__"]}}, {"id": "OTU_93", "metadata": {"taxonomy": ["k__", "p__", "c__", "o__", "f__Psychromonadaceae", "g__", "s__"]}}, {"id": "OTU_94", "metadata": {"taxonomy": ["k__", "p__", "c__", "o__", "f__Desulfobacteraceae", "g__", "s__"]}}, {"id": "OTU_95", "metadata": {"taxonomy": ["k__", "p__", "c__", "o__", "f__Gordoniaceae", "g__", "s__"]}}, {"id": "OTU_96", "metadata": {"taxonomy": ["k__", "p__", "c__", "o__", "f__Moraxellaceae", "g__", "s__"]}}, {"id": "OTU_97", "metadata": {"taxonomy": ["k__", "p__", "c__", "o__", "f__Nocardiaceae", "g__", "s__"]}}], "matrix_type": "sparse", "matrix_element_type": "int", "type": "OTU table", "columns": [{"id": "Essaijanv2013-60", "metadata": {"phinchID": "Essaijanv2013-60"}}, {"id": "Essaijanv2013-12", "metadata": {"phinchID": "Essaijanv2013-12"}}, {"id": "Essaijanv2013-57", "metadata": {"phinchID": "Essaijanv2013-57"}}, {"id": "Essaijanv2013-82", "metadata": {"phinchID": "Essaijanv2013-82"}}, {"id": "Essai2015-112", "metadata": {"phinchID": "Essai2015-112"}}, {"id": "Essaijanv2013-130", "metadata": {"phinchID": "Essaijanv2013-130"}}, {"id": "Essaijanv2013-58", "metadata": {"phinchID": "Essaijanv2013-58"}}, {"id": "Essaijanv2013-129", "metadata": {"phinchID": "Essaijanv2013-129"}}, {"id": "Essai2015-120", "metadata": {"phinchID": "Essai2015-120"}}, {"id": "Essai2015-132", "metadata": {"phinchID": "Essai2015-132"}}, {"id": "Essaijanv2013-80", "metadata": {"phinchID": "Essaijanv2013-80"}}, {"id": "Essaijanv2013-128", "metadata": {"phinchID": "Essaijanv2013-128"}}, {"id": "Essaijanv2013-131", "metadata": {"phinchID": "Essaijanv2013-131"}}, {"id": "Essai2015-134", "metadata": {"phinchID": "Essai2015-134"}}, {"id": "Essai2015-135", "metadata": {"phinchID": "Essai2015-135"}}, {"id": "Essai2015-113", "metadata": {"phinchID": "Essai2015-113"}}, {"id": "Essaijanv2013-10", "metadata": {"phinchID": "Essaijanv2013-10"}}, {"id": "Essaijanv2013-11", "metadata": {"phinchID": "Essaijanv2013-11"}}, {"id": "Essaijanv2013-81", "metadata": {"phinchID": "Essaijanv2013-81"}}, {"id": "Essai2015-110", "metadata": {"phinchID": "Essai2015-110"}}, {"id": "Essai2015-133", "metadata": {"phinchID": "Essai2015-133"}}, {"id": "Essaijanv2013-83", "metadata": {"phinchID": "Essaijanv2013-83"}}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundanceTable_to_biom/test-data/merge_summary_reads.csv Tue Mar 20 04:21:57 2018 -0400 @@ -0,0 +1,98 @@ +Order,Essaijanv2013-60,Essaijanv2013-12,Essaijanv2013-57,Essaijanv2013-82,Essai2015-112,Essaijanv2013-130,Essaijanv2013-58,Essaijanv2013-129,Essai2015-120,Essai2015-132,Essaijanv2013-80,Essaijanv2013-128,Essaijanv2013-131,Essai2015-134,Essai2015-135,Essai2015-113,Essaijanv2013-10,Essaijanv2013-11,Essaijanv2013-81,Essai2015-110,Essai2015-133,Essaijanv2013-83 +Acholeplasmataceae,12,13,34,8,16,42,31,29,23,16,56,56,39,15,18,10,12,9,7,29,20,37 +Acidaminococcaceae,158,169,170,135,122,127,188,146,138,124,170,136,152,149,121,139,173,163,160,125,142,143 +Actinomycetaceae,8,8,6,6,8,7,8,7,7,8,9,8,7,6,6,7,9,7,9,7,9,7 +Aerococcaceae,30,48,45,40,41,48,48,43,60,49,45,52,50,37,42,40,48,41,56,45,45,39 +Alicyclobacillaceae,2,5,2,1,2,1,1,1,5,4,NA,1,2,4,4,3,2,1,1,3,5,3 +Bacillaceae,42,62,55,42,55,58,67,59,75,84,53,52,44,44,57,51,72,47,56,69,87,40 +Bacteroidaceae,92,102,79,89,86,92,90,75,92,75,84,86,83,78,75,106,92,87,89,85,98,93 +Bifidobacteriaceae,43,52,46,40,44,50,63,51,47,49,51,44,42,53,42,44,55,45,52,41,57,41 +Burkholderiaceae,2,5,4,3,NA,2,3,1,1,3,4,3,1,2,2,2,5,3,2,1,1,1 +Campylobacteraceae,2,2,1,1,1,1,1,1,3,3,2,3,2,3,2,4,3,1,1,3,5,2 +Carnobacteriaceae,3,4,2,2,1,1,4,2,5,3,3,1,1,2,1,2,4,3,5,4,3,1 +Clostridiaceae,2274,2954,2550,2234,2212,2705,3156,2731,2853,2982,2666,2447,2444,2344,2436,2510,2945,2569,2680,2612,3288,2094 +Clostridiales Family XI. Incertae Sedis,99,144,111,99,106,124,139,121,134,135,117,110,98,113,106,114,136,112,129,132,167,107 +Coriobacteriaceae,247,330,270,239,197,223,349,220,259,294,293,236,229,251,231,229,336,254,273,224,355,249 +Corynebacteriaceae,1,NA,NA,1,1,1,1,1,NA,1,NA,NA,1,NA,1,1,1,1,1,NA,1,1 +Dehalococcoidaceae,11,13,8,10,1,13,14,11,9,5,7,3,12,9,7,10,5,9,6,5,3,11 +Desulfovibrionaceae,49,19,219,6,114,3,152,41,141,278,205,71,10,28,172,27,65,14,71,179,304,5 +Dietziaceae,1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +Elusimicrobiaceae,4,8,41,NA,NA,NA,1,2,NA,NA,35,95,29,NA,NA,NA,NA,15,NA,NA,1,2 +Enterobacteriaceae,185,852,908,83,413,68,785,314,464,172,1002,975,535,541,471,457,881,222,137,391,617,83 +Enterococcaceae,34,35,36,31,25,37,39,34,28,32,33,34,28,34,27,26,34,37,32,32,36,29 +Erysipelotrichaceae,2495,2605,1598,1664,2558,1484,2043,1452,2969,3223,2142,1450,1891,2864,2908,2899,2291,1712,2513,2842,3325,2384 +Eubacteriaceae,3170,3577,3008,3188,2998,3759,3733,3628,3924,3749,3311,3062,3223,3379,3265,3216,3885,3015,3750,3827,4131,2927 +Fabaceae,1,NA,NA,1,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA,1,NA,NA,NA,NA,NA +Fibrobacteraceae,3,2,2,1,3,2,2,NA,3,3,4,1,1,2,2,4,2,3,3,3,4,1 +Flavobacteriaceae,2,4,4,3,5,2,5,5,4,5,4,4,3,4,4,6,2,2,3,6,4,3 +Fusobacteriaceae,5,7,7,7,10,6,6,5,10,9,8,4,6,7,7,7,9,7,9,7,11,5 +Halobacteriaceae,1,NA,NA,1,NA,NA,1,NA,1,NA,NA,NA,1,NA,NA,1,1,NA,1,NA,1,1 +Helicobacteraceae,2,2,2,2,2,NA,2,1,3,3,NA,1,3,2,1,2,3,NA,1,5,4,1 +Heliobacteriaceae,2,2,3,1,1,3,1,2,1,2,2,1,1,1,2,3,1,1,2,NA,4,2 +Lachnospiraceae,23534,32008,27796,28379,26347,33606,32757,33216,33293,30719,31872,30047,31495,26754,27875,26243,30945,30700,32188,28949,34384,26978 +Lactobacillaceae,71,82,63,37,56,67,79,39,55,77,48,33,47,109,79,48,62,70,52,55,97,53 +Leptotrichiaceae,3,3,4,5,4,4,7,4,6,7,4,5,3,3,4,6,6,4,4,5,8,4 +Leuconostocaceae,5,6,3,3,9,4,4,2,11,13,2,1,5,13,10,8,5,3,3,7,14,5 +Methanobacteriaceae,15,26,32,21,27,34,33,42,28,27,35,30,21,19,22,23,27,25,31,32,30,21 +Methanomicrobiaceae,1,1,NA,NA,1,2,NA,2,1,2,NA,1,1,2,2,2,NA,NA,NA,NA,2,NA +Methanosarcinaceae,2,NA,NA,NA,3,4,4,4,4,5,NA,5,2,5,5,5,2,NA,2,2,5,NA +Micromonosporaceae,1,1,NA,NA,NA,1,1,1,NA,NA,1,1,1,NA,NA,1,NA,1,1,NA,1,1 +Mycoplasmataceae,1,NA,2,NA,3,1,NA,NA,NA,4,2,NA,NA,NA,2,2,2,NA,1,3,1,1 +Nitrospiraceae,2,NA,NA,1,NA,NA,1,1,1,1,NA,NA,NA,1,NA,NA,2,1,NA,NA,NA,1 +Oxalobacteraceae,1,NA,3,1,1,1,3,NA,1,1,3,1,NA,NA,NA,NA,NA,NA,1,NA,2,NA +Paenibacillaceae,14,21,20,15,12,18,20,13,17,20,18,16,13,8,6,12,16,10,21,13,20,11 +Parachlamydiaceae,1,NA,1,NA,1,1,1,1,1,1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA +Pasteurellaceae,8,10,9,12,9,13,12,15,11,10,10,15,17,9,10,8,12,11,14,10,12,15 +Peptococcaceae,306,339,325,233,268,270,386,306,334,345,317,294,254,259,270,273,351,282,302,331,431,221 +Peptostreptococcaceae,1513,2178,1594,886,1963,870,1355,1003,2593,2795,954,995,1270,2382,2449,2324,1700,1208,714,1877,2705,1397 +Planctomycetaceae,5,4,11,6,5,8,10,7,10,9,10,3,5,3,6,7,15,6,7,11,6,NA +Poaceae,11,8,6,18,1,13,10,7,1,1,8,20,11,4,1,6,11,8,8,1,8,12 +Porphyromonadaceae,430,461,446,459,383,442,456,398,432,386,421,407,410,372,361,428,440,443,449,403,428,405 +Prevotellaceae,979,937,940,1042,881,1064,887,901,968,745,1018,867,993,757,709,924,963,917,932,910,945,1075 +Rhizobiaceae,1,NA,NA,NA,NA,NA,1,NA,NA,NA,1,NA,1,NA,NA,NA,NA,NA,NA,NA,NA,NA +Rhodobacteraceae,1,NA,1,2,1,2,2,2,1,1,2,1,2,1,1,NA,NA,3,1,1,1,2 +Rhodospirillaceae,11,4,1,13,11,15,5,14,14,13,8,6,14,1,7,1,NA,10,9,4,15,12 +Rikenellaceae,39,62,48,34,50,42,47,31,50,53,38,29,32,38,34,67,55,44,37,46,64,33 +Ruminococcaceae,23852,26024,23962,21997,19422,24480,30028,25215,23616,23167,26797,22344,22253,22676,20511,22671,28715,23477,26118,22789,26354,22177 +Sphingobacteriaceae,3,3,4,3,3,3,4,4,5,5,3,4,4,3,3,4,4,4,3,5,5,3 +Spirochaetaceae,82,98,85,72,91,79,122,106,100,101,96,86,83,67,74,74,100,98,100,101,120,58 +Staphylococcaceae,4,5,5,2,4,4,3,3,5,10,5,3,3,5,9,5,4,3,2,3,9,3 +Streptococcaceae,125,142,124,100,126,108,134,84,147,153,114,119,136,162,169,132,150,90,66,158,183,106 +Streptomycetaceae,1,2,1,1,1,2,4,2,1,NA,NA,1,1,2,2,2,4,3,2,2,1,1 +Succinivibrionaceae,1,5,5,1,NA,3,6,4,2,1,3,3,3,2,NA,2,5,2,3,1,3,NA +Sutterellaceae,21,5,3,28,49,57,29,59,47,43,7,28,64,81,41,96,11,8,4,44,67,41 +Synergistaceae,20,19,26,17,21,22,26,22,24,21,23,17,19,22,18,24,30,27,20,21,30,15 +Syntrophomonadaceae,47,61,51,38,39,41,55,43,50,45,43,39,38,41,44,44,51,46,44,47,53,40 +Thermoanaerobacteraceae,12,12,7,7,7,7,14,8,8,9,8,8,7,9,7,9,12,9,9,12,14,5 +Thermoanaerobacterales Family III. Incertae Sedis,13,21,20,12,18,13,23,20,26,24,13,12,14,12,12,15,23,16,23,28,24,12 +Thermotogaceae,1,2,2,NA,1,1,2,1,3,2,2,1,1,NA,2,1,2,2,2,2,3,1 +Veillonellaceae,575,530,706,486,480,491,569,492,530,614,544,466,466,560,526,545,569,497,522,515,583,485 +Verrucomicrobiaceae,2,2,1,1,2,1,3,2,1,NA,1,2,1,NA,NA,NA,2,2,1,1,2,1 +Victivallaceae,2,3,1,2,8,3,2,3,4,6,2,5,1,1,6,3,4,1,2,6,13,NA +Anaeroplasmataceae,NA,1,2,1,1,3,2,2,1,NA,2,3,2,1,1,1,NA,1,1,1,1,2 +Aquificaceae,NA,1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA,NA,1,NA +Comamonadaceae,NA,1,NA,1,1,1,1,1,1,2,1,1,1,1,1,2,NA,NA,1,1,2,1 +Cytophagaceae,NA,1,NA,1,NA,NA,1,NA,NA,NA,NA,NA,NA,NA,1,NA,NA,NA,NA,NA,NA,NA +Halanaerobiaceae,NA,1,1,NA,NA,1,NA,NA,NA,NA,1,1,NA,NA,NA,NA,NA,1,1,NA,NA,NA +Listeriaceae,NA,1,1,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,1,NA,NA,NA,NA,NA,NA,NA,NA +Methanococcaceae,NA,1,1,1,NA,1,1,NA,NA,1,NA,1,NA,NA,NA,NA,1,NA,NA,NA,NA,NA +Alcaligenaceae,NA,NA,1,1,1,NA,1,NA,1,NA,1,NA,NA,1,NA,NA,NA,NA,1,1,1,NA +Micrococcaceae,NA,NA,2,2,2,3,1,1,NA,1,1,2,2,2,2,1,1,4,1,1,4,NA +Neisseriaceae,NA,NA,1,NA,NA,NA,NA,1,1,1,1,1,1,NA,1,NA,NA,1,1,1,1,NA +Propionibacteriaceae,NA,NA,1,NA,1,NA,NA,NA,NA,2,NA,1,NA,NA,NA,NA,NA,NA,NA,1,NA,NA +Pseudonocardiaceae,NA,NA,1,NA,1,NA,1,NA,NA,1,1,NA,NA,NA,NA,NA,1,NA,NA,NA,1,NA +Trichocomaceae,NA,NA,5,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +Chlorobiaceae,NA,NA,NA,1,NA,NA,1,NA,1,NA,NA,NA,NA,NA,NA,1,NA,NA,1,NA,1,NA +Deferribacteraceae,NA,NA,NA,1,NA,1,NA,NA,NA,NA,NA,1,1,NA,NA,NA,NA,1,NA,NA,1,NA +Trypanosomatidae,NA,NA,NA,NA,1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +Vibrionaceae,NA,NA,NA,NA,1,1,NA,NA,1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA +Desulfohalobiaceae,NA,NA,NA,NA,NA,NA,1,NA,NA,NA,NA,NA,NA,1,NA,NA,1,1,NA,NA,NA,NA +Methanoregulaceae,NA,NA,NA,NA,NA,NA,1,1,NA,1,NA,NA,NA,1,1,NA,NA,NA,NA,NA,1,NA +Bradyrhizobiaceae,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA,1,1,NA,1,1,NA,NA,NA,NA,NA,1 +Clostridiales Family XVIII. Incertae Sedis,NA,NA,NA,NA,NA,NA,NA,NA,1,1,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA +Desulfobulbaceae,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +Psychromonadaceae,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,1,NA,NA,NA,NA,1,NA,NA,NA,NA,NA +Desulfobacteraceae,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,1,NA,NA,1,NA,1,NA,NA +Gordoniaceae,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA,NA,NA,1,1,NA,NA,NA +Moraxellaceae,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA,NA,NA,NA,NA,NA,NA,NA +Nocardiaceae,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1,NA,NA,NA,NA,NA,NA