qiime2lefse1

Determine features of organisms, clades, taxonomic units, genes

Usage

qiime2lefse [-h] [--in [INPUT_FILE]] [--md [METADATA_FILE]] [--out [OUTPUT_FILE]] [-c class attribute] [-s subclass attribute] [-u subject attribute]

Overview

Script will convert QIIME TSV BIOM table for use with lefse. It is imperative that this table has taxa metadata associated with it named 'Consensus Lineage', this can be down with e.g. the follow biom convert script: ---- biom convert -i otu.biom -o otu.txt --to-tsv --header-key Taxonomy --outputmetadata-id 'Consensus Lineage'

Options

optional arguments:

-h, --help: show this help message and exit

--in [INPUT_FILE]: the Qiime OTU table file [ stdin if not present ]

--md [METADATA_FILE]: the Qiime OTU table file [ only OTU table without metadata if not present ]

--out [OUTPUT_FILE]: the output file [stdout if not present]

`-c class attribute`	the attribute to use as class
`-s subclass attribute`	the attribute to use as subclass
`-u subject attribute`	the attribute to use as subject