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.