Filter-metabolic

This script filters the output of METABOLIC to extract features present in abundant MAGs only.

1. Select MAGs with an abundance higher than the user-specified threshold.
2. Select the features present in at least 1 of the abundant MAGs.

Requirements

• pandas library for python. OS, argparse modules from the standard library.

Input

• The abundances file.
• The 6 separate .tsv worksheets, output of METABOLIC.

Abundances file

Please use the provided template file and fill it in with your data. A tab-separated .csv file with the abundance of each MAG in the samples.

• You can name the sample columns with the name of your samples.
• A MAG will be selected if it's more abundant than threshold in at least 1 sample.
• You can remove unused sample columns, and you can add other sample columns if you have more than 2 samples.
• In the taxonomy column you can provide taxonomy associated to each MAG.

Output

The files are created into the folder <prefix>_filter_METABOLIC.

• abundant_mags.csv: .csv file with the abundant MAG only.
• The 6 filtered .tsv worksheets. Optionally, the MAG id will be replaced with the associated taxonomy provided in the abundances file.

Usage

$ ./filter_metabolic.py <MAG abundances .csv> -f <folder with METABOLIC worksheets> -t <abundance threshold> -o <output folder prefix> -x

• <MAG abundances .csv>: is the only required argument. It's the file with the abundances of MAGs.
• <folder with METABOLIC worksheets>: is the folder where the METABOLIC worksheets are stored. Defaults to CWD.
• <abundance threshold>: the minimum abundance for a MAG to be selected as abundant. Defaults to 1.
• <output folder prefix>: prefix added to "filter_METABOLIC" name for the folder containing the output.
• -x: if set the script will perform the taxonomy replacement.