qiime_to_lefse

Convert Qiime taxa tables and mapping files to a LEfSe formatted file

Description

This script was created in order to convert the Qiime pipeline files to LEfSe format easily. The script takes a Qiime mapping file and a Qiime OTU abundance table, along with any number of categories and will output a LEfSe table.

Categories must be comma separated

The default behavior is to collapse the unassigned reads during scrubbing of the original taxa headers ("k", "p", "c", "o", "f", "g", "s__"). The --clean option will remove the "Other" classification and sum the abundances with any name-collision it encounters.

Usage:

python qiime_to_lefse.py -m mappingfile.txt -t otus_L3.txt -c category1,category2,category3 -o converted_lefse.txt --clean