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MetaPhlAn3 filtretion by taxonomical level

What is this?

This tool sorts and merges multiple MetaPhlAn3 output table files and creates a tab-seperated-value (.tsv) file with all results of the provided taxonomical level. At the end of the process all given MetaPhlAn3 output files will be sorted into /unknown and /results folders, where /unknown folder will contain all 100% unknown (unmatched) results files.

INPUT: multiple MetaPhlAn3 output table files (Text file, usually ends with '.out')
OUTPUT: A single file, containing all organisms from provided files, fileterd to provided taxonomical level

How to use?

Commands

  • Run tool (usage):
    ./metaphlan_runner <mpa_results.txt | folder/with/mpa/results> -f <taxonomical level> -o <out/dir/> [ADDITIONAL FLAGS][--help]

Examples

  • Run tool on all mpa3 results in folder my/mpa/folder and filter only species (-f s). output results to myResults/folder
    ./metaphlan_runner my/mpa/folder -f s -o myResults/folder
  • Run tool as in 1st example, but copy (-c) mpa3 results to output destination. (default will move them there)
    ./metaphlan_runner my/mpa/folder -f s -o myResults/folder -c
  • Run tool on mpa1.txt and mpa2.txt only and filter only by kingdom (-f k). output results to myResults/folder
    ./metaphlan_runner mpa1.txt mpa2.txt -f k -o myResults/folder
  • View tool help
./metaphlan_runner  --help

Flags and running options

To see more options and flags please run: --help -h -H ---> View help and exit. --copy -c ---> Copy mpa3 results instead of moving them.

All available filters:

k=kingdom
p=phylum
c=class
o=order
f=family
g=genus
s=species