Quick StartΒΆ

In order to run ProkFunFind on your genome as soon as you have installed it, you can simply follow the next steps:

  • Type: prokfunfind -h to see all options available. All command-line options are described below:

usage: prokfunfind [-h] -f  -o  [-p] -g

Identify genes related functions of interest

optional arguments:
  -h, --help            show this help message and exit
  -f , --function       Path to configuration file
  -o , --outputprefix   The output file name prefix
  -p , --processes      Number of genomes to process concurrently (default=1)
  -g , --gtab           Table of genomes to search

  • On a completely assembled genome (for example the representative EBI genome) run a command like the following: prokfunfind -f config.yaml -g genome.inputs -o output.prefix

This command will will detect the function Function in a genome or set of genomes designated in a genome table (genome.inputs) based on the function defined in the config.yaml file and outputs the result in output.prefix

To test your installation of ProkFunFind you can run the following command on some sample data included with the repository:

prokfunfind -f {path to PFF repository}/ProkFunFind/data/HDC/config.yaml --gtab {path to PFF repository}/ProkFunFind/data/genome-table.tsv -o tmp

This command should print an output to the screen that looks like:

INFO:root:Checking configuration files
INFO:root:Searching for function
INFO:root:Identifying gene clusters
INFO:root:Summarizing function presence and genes
Failed to detect function: HDC in genome {path to ProkFunFind}/ProkFunFind/data/./test-genome//GTDB18040
1 out of 2 essential components present
0 out of 0 nonessential components present

This command will also produce multiple output files with the names tmp.GTDB18040*

See the other sections of the documents for descriptions of each of these files.