Greg Caporaso gregcaporaso

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'))"

This depends on biom version >= 2.1.5, < 2.2.0 and vsearch >= 1.7.0.

Please note that all of this is highly experimental. I'm keeping these notes as I work with this approach. For published work, I still recommend using standard pipelines, such as those in QIIME 1.9.1.

$ biom --version
biom, version 2.1.5

$ vsearch --version
vsearch v1.7.0_osx_x86_64, 16.0GB RAM, 8 cores

	#!/usr/bin/env python
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	# Auto-generated by provenance_lib v.0.2.0 at 09:49:20 AM on 24 Jan, 2023

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