Prophage finder using multiple metrics
#What is PhiSpy?
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions.
Initial versions of PhiSpy were written by
Improvements, bug fixes, and other changes were made by
PhiSpy requires following programs to be installed in the system. Most of these are likely already on your system.
Python- version 3.4 or later
Biopython- version 1.58 or later
gcc- GNU project C and C++ compiler - version 4.4.1 or later
Python.hheader file. This is included in
python3-devthat is available on most systems.
For a brand new
Ubuntu installation (e.g. on Google Cloud Platform you can install these dependencies with these commands:
sudo apt install -y build-essential python3-dev python3-pip python3 -m pip install --user PhiSpy
This will install
~/.local/bin which should be in your
$PATH but might not be (see this detailed discussion).
If you try
PhiSpy.py -v and get an error like this:
$ PhiSpy.py -v -bash: PhiSpy.py: command not found
Then you can either use the full path:
or add that location to your
echo "export PATH=\$HOME/.local/bin:\$PATH" >> ~/.bashrc source ~/.bashrc PhiSpy.py -v
For advanced users, you can clone the git repository and use that (though
pip is the recommended install method).
git clone https://github.com/linsalrob/PhiSpy.git cd PhiSpy` python3 setup.py install --user
If you have root and you want to install globally, you can change the setup command.
git clone https://github.com/linsalrob/PhiSpy.git cd PhiSpy` python3 setup.py install
For ease of use, you may wish to add the location of PhiSpy.py to your $PATH.
Download the Streptococcus pyogenes M1 genome
curl -Lo Streptococcus_pyogenes_M1_GAS.gb https://bit.ly/37qFArb PhiSpy.py -o Streptococcus.phages Streptococcus_pyogenes_M1_GAS.gb
or to run it with the
Streptococcus training set:
PhiSpy.py -o Streptococcus.phages -t data/trainSet_160490.61.txt Streptococcus_pyogenes_M1_GAS.gb
This uses the
GenBank format file for Streptococcus pyogenes M1 GAS that we provide in the tests/ directory, and we use the training set for S. pyogenes M1 GAS that we have pre-calculated. This quickly identifies the four prophages in this genome, runs the repeat finder on all of them, and outputs the answers.
You will find the output files from this query in
The simplest command is:
PhiSpy.py -f genbank_file -o output_directory
genbank file: The input DNA sequence file in GenBank format.
output directory: The output directory is the directory where the final output file will be created.
After annotation, you can download the genome directory from the server.
For the help menu use the
python PhiSpy.py -h
There are 3 output files, located in output directory.
prophage.tbl: This file has two columns separated by tabs [id, location]. The id is in the format: pp_number, where number is a sequential number of the prophage (starting at 1). Location is be in the format: contig_start_stop that encompasses the prophage.
prophage_tbl.tsv: This is a tab seperated file. The file contains all the genes of the genome. The tenth colum represents the status of a gene. If this column is 1 then the gene is a phage like gene; otherwise it is a bacterial gene.
This file has 16 columns:(i) fig_no: the id of each gene; (ii) function: function of the gene; (iii) contig; (iv) start: start location of the gene; (v) stop: end location of the gene; (vi) position: a sequential number of the gene (starting at 1); (vii) rank: rank of each gene provided by random forest; (viii) my_status: status of each gene based on random forest; (ix) pp: classification of each gene based on their function; (x) Final_status: the status of each gene. For prophages, this column has the number of the prophage as listed in prophage.tbl above; If the column contains a 0 we believe that it is a bacterial gene. If we can detect the att sites, the additional columns will be: (xi) start of attL; (xii) end of attL; (xiii) start of attR; (xiv) end of attR; (xv) sequence of attL; (xvi) sequence of attR.
- prophage_coordinates.tsv: This file has the prophage ID, contig, start, stop, and potential att sites identified for the phages.
- Streptococcus pyogenes M1 GAS which has a single genome contig. The genome contains four prophages.
To analyze this data, you can use:
PhiSpy.py -o output_directory -t data/trainSet_160490.61.txt tests/Streptococcus_pyogenes_M1_GAS.gb
And you should get a prophage table that has this information (for example, take a look at
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
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