Assessing capacity to synthesize or degrade specific compounds among a large set of bacterial metabolic networks and screen them accordingly.

This workflow is licensed under the GNU GPL-3.0-or-later, see the LICENSE file for details.

Prolipipe relies on outputs from the "AuFAMe" package It runs with python >= 3.8.

These python packages are needed :

• pandas
• numpy
• plotly
• glob2
• jupyter
• papermill
• padmet

Prolipipe also needs Quarto to generate the interactive report (version > 1.7).

Prolipipe is available on the conda channel "fermentsdufutur" and can be installed with:

conda create -n prolipipe
conda activate prolipipe
conda install -c fermentsdufutur prolipipe

Prolipipe and AuFAMe rely on data about genomes, either a taxonomic ID for building accurate GSMs in the case of AuFAMe or species name and assembly level categories for clustering during Prolipipe's analyses. A compatible structure for both is the following columns in a tsv file :

• "Species" : space-separated species name (used to categorize genomes in reports and heatmaps)
• "Taxon_id" : strict taxID of the species ; can be "2" (Bacteria) if ignored
• "Filename" : strict name of the genome file, without file extension
• "Strain" : space-separated strain name
• "Status" : another metric to categorize genomes based on assembly quality ; that way, can be either "Complete", "Chromosome", "Scaffold" and "Contig"

To run Prolipipe with padmet files from AuFAMe as input, generate TSV files and an interactive Quarto report:

prolipipe -pad DIRECTORY --tax TAXFILE --pwy PWY_FOLD

To generate TSV files without the Quarto report:

prolipipe -pad DIRECTORY --tax TAXFILE --pwy PWY_FOLD --no-report

To run Prolipipe with TSV files from AuFAMe as input and generate an interactive Quarto report:

prolipipe -i DIRECTORY --tax TAXFILE --pwy PWY_FOLD

To regenerate Quarto report from TSV files created by Prolipipe:

prolipipe-report -i DIRECTORY -d OUT_DIRECTORY