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@gregcaporaso gregcaporaso/notes.md
Last active Nov 10, 2015

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What would you like to do?
convert biom observation counts to per-sample rank abundances

You'll need to install master of biom-format to use this until the 2.1.6 release is posted (at which point that milestone will be closed, and you can skip this step if you're using biom-format >=2.1.6, < 2.2.0), which you can do as follows:

pip install https://github.com/biocore/biom-format/archive/master.zip

Then, run the following command, substituting your file names for in.biom and out.biom:

python -c "from biom import load_table; t = load_table('in.biom'); t.rankdata(); t.to_json('biom 2.1.5-dev', direct_io=open('out.biom','w'))"
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