Scripts for processing FACoP/FUNAGE-Pro input/output

These scripts are used for creating the input for the bacterial annotation tool FACoP (http://facop.molgenrug.nl/) and the Gene Set Enrichment tool FUNAGE-Pro (http://funagepro.molgenrug.nl/).

Preprocessing files for annotation with FACoP

Important: Most bacterial genome can be annotated as-is with FACoP as long as the .gff and .fasta are given and the genome size is below 10 Mbp.

For longer Genomes the .fasta and .gff files need to be split.

usage: python facop_preprocessing.py [-h] [-o OUTPUT] fasta gff threshold

The FACoP webserver only provides annotations for genomes with a length smaller than 10 Mbp. This tool creates artificial contigs below a specified length threshold that
can be used as input. It preferably splits the file into existing contigs but if a single contig is above the threshold it will be cut between genes.

positional arguments:
  fasta                 fasta file to split
  gff                   gff file to split
  threshold             maximum length of resulting contigs

options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        output folder

Post-processing files after enrichment with FUNAGE-Pro

Transforms the columns of the FUNAGE-Pro output and saves the result as an .xlsx file

usage: python funage_postprocessing.py [-h] [-o OUTPUT] input

Enhances the output table of FUNAGE-Pro and saves it to .xlsx files. Please make sure to export all columns in FUNAGE-Pro

positional arguments:
  input                 folder containing FUNAGE-Pro files

options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        output folder

Transforming FACoP annotation for usage in GO-Compass

Go-Compass (https://go-compass-tuevis.cs.uni-tuebingen.de/) requires a transformation of the GO Annotation that can be done with this script.

usage: python facop_to_gocompass.py [-h] input output

Transforms FACoP GO annotation to the annotation format used by GO-Compass

positional arguments:
  input       .tsv or .txt containing GO annotation created by FACoP
  output      Name of output file

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