Convert table to biom with taxonomy assignment information(转换table生成包含分类学的biom文件)
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