fCAT

Python package for fCAT, a feature-aware Completeness Assessment Tool

Table of Contents

• How to install
• Usage
• Output
• Bugs
• Contributors
• Contact

How to install

fCAT tool is distributed as a python package called fcat. It is compatible with Python ≥ v3.7.

You can install fcat using pip:

# python3 -m pip install fcat
python3 -m pip install git+https://github.com/BIONF/fCAT

or, in case you do not have admin rights, and don't use package systems like Anaconda to manage environments you need to use the --user option:

# python3 -m pip install --user fcat
python3 -m pip install --user git+https://github.com/BIONF/fCAT

and then add the following line to the end of your ~/.bashrc or ~/.bash_profile file, restart the current terminal to apply the change (or type source ~/.bashrc):

export PATH=$HOME/.local/bin:$PATH

Usage

The complete process of fCAT can be done using one function fcat

fcat --coreDir /path/to/fcat_data --coreSet eukaryota --refspecList "HOMSA@9606@2" --querySpecies /path/to/query.fa [--annoQuery /path/to/query.json] [--outDir /path/to/fcat/output]

where eukaryota is name of the fCAT core set (equivalent to BUSCO set); HOMSA@9606@2 is the reference species from that core set that will be used for the ortholog search; query is the name of species of interest. If --annoQuery not specified, fCAT fill do the feature annotation for the query proteins using FAS tool.

Output

You will find the output in the /path/to/fcat/output/fcatOutput/eukaryota/query/ folder, where /path/to/fcat/output/ could be your current directory if you not specified --outDir when running fcat. The following important output files/folders can be found:

- all_summary.txt: summary of the completeness assessment using all 4 score modes
- fdogOutput.tar.gz: a zipped file of the ortholog search result
- mode_1, mode_2, mode_3 and mode_4: detailed output for each score mode
- phyloprofileOutput: output phylogenetic profile data that can be used with [PhyloProfile tool](https://github.com/BIONF/PhyloProfile)

For internal use

fCAT algorithm consists of 3 main steps:

1. Calculate group-specific cutoffs for a core set

Please make sure that the R dependencies are available before running this function.

fcat.cutoff --coreDir /path/to/fcat_data --coreSet eukaryota

2. Search for orthologs in a gene set of interst and create phylogenetic profiles

fcat.ortho --coreDir /path/to/fcat_data --coreSet eukaryota --refspecList "HOMSA@9606@2" --querySpecies /path/to/query.fa --annoQuery /path/to/query.json

3. Create report for completeness assessment

fcat.report --coreDir /path/to/fcat_data --coreSet eukaryota --outDir /path/to/fcat/output --queryID queryID --mode 1

Bugs

Any bug reports or comments, suggestions are highly appreciated. Please open an issue on GitHub or be in touch via email.

Contributors

• Vinh Tran
• Giang Nguyen

Contact

For further support or bug reports please contact: [email protected]