Convert table to biom with taxonomy assignment inf

格式转换工具,将table格式转换为biom格式,并添加OTU物种分类信息

输入文件:

OUT Table file

OTU ID     Bio1 Bio2 Bio3 Bio4 Bio5 Bio6 Bio7 Bio8 Bio9 Bio10

OTU1        0       0       0       0       0       6       34     104  367  254

OTU2        52     335  18     49     0       0       0       0       0       0

OTU3        0       0       0       0       5       0       0       0       0       0

Taxonomy Assignment file

OTU1        d__Bacteria; p__Bacteroidetes; c__Cytophagia; o__Cytophagales; f__Cytophagaceae; g__Ohtaekwangia; s__uncultured_bacterium

OTU2        d__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Methylobacteriaceae; g__Methylobacterium

OTU3        d__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__DB1-14; f__norank; g__norank; s__uncultured_bacterium

输出文件:

biom格式的OTU Table文本文件,其中包含OTU的物种分类信息。

biom格式参考:http://biom-format.org/

相关文献如下所示:

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso.GigaScience 2012, 1:7. doi:10.1186/2047-217X-1-7