fcat 0.0.8

Python package for fCAT, a feature-aware completeness assessment tool

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

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

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: folder contains output phylogenetic profile data that can be used with PhyloProfile tool

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: [e-mail]