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#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

Sajia Akhter (sajia@stanford.edu) Edwards Bioinformatics Lab

Improvements, bug fixes, and other changes were made by

Katelyn McNair Edwards Bioinformatics Lab and Przemyslaw Decewicz
University of Warsaw



SOFTWARE REQUIREMENTS


PhiSpy requires following programs to be installed in the system. Most
of these are likely already on your system.

1.  Python - version 3.4 or later
2.  Biopython - version 1.58 or later
3.  gcc - GNU project C and C++ compiler - version 4.4.1 or later
4.  The Python.h header file. This is included in python3-dev that is
    available on most systems.



INSTALLATION


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 PhiSpy.py in ~/.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:

    ~/.local/bin/PhiSpy.py -v

or add that location to your $PATH:

    echo "export PATH=\$HOME/.local/bin:\$PATH" >> ~/.bashrc
    source ~/.bashrc
    PhiSpy.py -v


Advanced Users

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.



TESTING PHISPY.PY


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 output_directory.



RUNNING PHISPY.PY


The simplest command is:

    PhiSpy.py -f genbank_file -o output_directory

where: - 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.

If you have new genome, we recommend annotating it using the RAST server
or PROKKA.

After annotation, you can download the genome directory from the server.



HELP


For the help menu use the -h option:

    python PhiSpy.py -h



OUTPUT FILES


There are 3 output files, located in output directory.

1.  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.

2.  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_.

3.  prophage_coordinates.tsv: This file has the prophage ID, contig,
    start, stop, and potential _att_ sites identified for the phages.



EXAMPLE DATA


-   _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 output_directory/prophage.tbl).

  Prophage number   Contig      Start     Stop
  ----------------- ----------- --------- ---------
  pp_1              NC_002737   529631    569288
  pp_2              NC_002737   778642    820599
  pp_3              NC_002737   1192630   1222549
  pp_4              NC_002737   1775862   1782822
