Phigaro: CLI tool for phage prediction

Phigaro is a scalable command-line tool for predictions phages and prophages from nucleid acid sequences (including metagenomes). It is based on phage genes HMMs and a smoothing window algorithm.

Requirements

• Python: Python 2.7, Python 3+ versions are supported. pip utility is also required (sudo apt-get install python-pip on Ubuntu).

• MetaGeneMark: Download it from http://topaz.gatech.edu/Genemark/license_download.cgi and follow the instructions.

• HMMER: Download it from http://hmmer.org/

• locate: In order to install Phigaro, you need locate. It is present in the latest Ubuntu distributions, but in case you don't have it, install it with sudo apt-get install locate

Installation

$ sudo -H pip install phigaro

If you have other pip versions installed, use pip2 or pip3 instead of pip

Configuration

Simplified, via phigaro-setup tool

In order to simplify setup process, you can run phigaro-setup tool. It will locate all needed software and download data.

Example:

$ phigaro-setup
[sudo] password for user:
Found MetaGeneMark in: /home/user/software/MetaGeneMark_linux_64/mgm/gmhmmp
Found MetaGeneMark model in: /home/user/software/MetaGeneMark_linux_64/mgm/MetaGeneMark_v1.mod
Found HMMER in: /home/user/software/hmmer-3.1b2-linux-intel-x86_64/binaries/hmmsearch
HMMER model in: /home/user/.phigaro/pvog/allpvoghmms
Downloading models to /home/user/.phigaro/pvog
Downloading http://download.ripcm.com/phigaro/allpvoghmms to /home/user/.phigaro/pvog/allpvoghmms
Downloading http://download.ripcm.com/phigaro/allpvoghmms.h3f to /home/user/.phigaro/pvog/allpvoghmms.h3f
Downloading http://download.ripcm.com/phigaro/allpvoghmms.h3i to /home/user/.phigaro/pvog/allpvoghmms.h3i
Downloading http://download.ripcm.com/phigaro/allpvoghmms.h3m to /home/user/.phigaro/pvog/allpvoghmms.h3m
Downloading http://download.ripcm.com/phigaro/allpvoghmms.h3p to /home/user/.phigaro/pvog/allpvoghmms.h3p

Manual

Create configuration file ~/.phigaro/config.yml with following content:

genemark:
  # Path to MetaGeneMark binary
  bin: /home/user/software/MetaGeneMark_linux_64/mgm/gmhmmp
  # Path to MetaGeneMark models
  mod_path: /home/user/software/MetaGeneMark_linux_64/mgm/MetaGeneMark_v1.mod
hmmer:
  # Path to HMMER hmmsearch binary
  bin: /home/user/software/hmmer-3.1b2-linux-intel-x86_64/binaries/hmmsearch
  # HMMER models, usually: ~/.phigaro/pvog/allpvoghmms
  pvog_path: /home/user/.phigaro/pvog/allpvoghmms
  e_value_threshold: 0.00445  # Do not change this
phigaro:
  threshold_max: 8.827586  # Do not change this
  threshold_min: 7.058859  # Do not change this
  window_len: 32  # Do not change this

Run phigaro-setup to download models data:

$ phigaro-setup
Phigaro already configured
Downloading models to /home/user/.phigaro/pvog
Downloading http://download.ripcm.com/phigaro/allpvoghmms to /home/user/.phigaro/pvog/allpvoghmms
Downloading http://download.ripcm.com/phigaro/allpvoghmms.h3f to /home/user/.phigaro/pvog/allpvoghmms.h3f
Downloading http://download.ripcm.com/phigaro/allpvoghmms.h3i to /home/user/.phigaro/pvog/allpvoghmms.h3i
Downloading http://download.ripcm.com/phigaro/allpvoghmms.h3m to /home/user/.phigaro/pvog/allpvoghmms.h3m
Downloading http://download.ripcm.com/phigaro/allpvoghmms.h3p to /home/user/.phigaro/pvog/allpvoghmms.h3p

or manually download data from http://download.ripcm.com/phigaro/

Usage

Getting help

$ phigaro -h  
usage: phigaro [-h] -f FASTA_FILE [-c CONFIG] [-o OUTPUT] [-t THREADS]
Phigaro is a scalable command-line tool for predictions phages and prophages                                                                                                                                                                        
from nucleid acid sequences

optional arguments:
  -h, --help            show this help message and exit
  -f FASTA_FILE, --fasta-file FASTA_FILE
                        Assembly scaffolds/contigs or full genomes, required
  -c CONFIG, --config CONFIG
                        Config file, not required
  -o OUTPUT, --output OUTPUT
                        Output file, not required, default is stdout
  -t THREADS, --threads THREADS
                        Num of threads (default is num of CPUs)

Searching prophages

$ phigaro -f Escherichia_coli_O157:H7_str._Sakai.fna
scaffold    begin   end 
>Escherichia_coli_O157:H7_str._Sakai    291589  317255
>Escherichia_coli_O157:H7_str._Sakai    881486  929292
>Escherichia_coli_O157:H7_str._Sakai    1042294 1075143
>Escherichia_coli_O157:H7_str._Sakai    1161297 1214167
>Escherichia_coli_O157:H7_str._Sakai    1242390 1312585
>Escherichia_coli_O157:H7_str._Sakai    1533217 1663713
>Escherichia_coli_O157:H7_str._Sakai    1755765 1806239
>Escherichia_coli_O157:H7_str._Sakai    1916035 1972127
>Escherichia_coli_O157:H7_str._Sakai    2154248 2251085
>Escherichia_coli_O157:H7_str._Sakai    2597642 2618313
>Escherichia_coli_O157:H7_str._Sakai    2666906 2713016
>Escherichia_coli_O157:H7_str._Sakai    2891705 2950968
>Escherichia_coli_O157:H7_str._Sakai    3476233 3498946
>Escherichia_coli_O157:H7_str._Sakai    5046510 5082381

Running time depends on the size of your input data and the number of CPUs used. The mean running time for a fasta file with Escherichia coli O157:H7 (str. Sakai) genome is 207 seconds (with 1 thread used).

Modus operandi

ORFs and corresponging proteins are predicted from the input .fasta file using MetaGeneMark. Phage genes are predicted with pVOG Hidden Markov Models that can be downloaded stand-alone from http://dmk-brain.ecn.uiowa.edu/pVOGs/. Each contig is represented as a sequence of phage and non-phage genes. A smoothing window algorithm determines regions with high density of phage genes and prophage boundaries.

In case of any questions regarding installing and running Phigaro please address estarikova@rcpcm.org or leave feedback on Github issues page.

(C) E.Starikova, N.Pryanichnikov, 2017