Metadata-Version: 2.1
Name: phigaro
Version: 0.2.1.4
Summary: Phigaro is a scalable command-line tool for predictions phages and prophages from nucleid acid sequences (including metagenomes) and is based on phage genes HMMs and a smoothing window algorithm.
Home-page: https://github.com/lpenguin/phigaro
Author: E.Starikova, N.Pryanichnikov, P.Tikhonova
Author-email: hed.robin@gmail.com
License: UNKNOWN
Description: # Phigaro
        Phigaro is a command-line tool for predictions phages and prophages from nucleid acid sequences (including metagenomes) and is based on phage genes HMMs (pVOG) and a smoothing window algorithm.
        
        ## Requirements
        Note, that in order to run Phigaro, you need to have Prodigal and HMMER installed.
        To install Prodigal, download it at https://github.com/hyattpd/Prodigal/wiki/installation and follow the instructions.
        To install HMMER, download it at http://hmmer.org/
        Also note that you need `locate` to successfully run setup. It is pre-installed in the latest Ubuntu distributions, but in case you don't have it, please run `sudo apt-get install locate`, it is a very useful tool.
        
        ## Installation
        
        ```
        sudo -H pip3 install phigaro
        ```
        then create a config file with:
        ```
        phigaro-setup
        ```
        It may take some time, since we are downloading the database
        
        ## Usage
        
        ```
        phigaro -h                                                                                                                                                                          15:04:32
        usage: phigaro [-h] [-V] -f FASTA_FILE [-c CONFIG] [-p] [-e EXTENSION [EXTENSION ...]] [-o OUTPUT] [--not-open] [-t THREADS]
        
        optional arguments:
          -h, --help            show this help message and exit
          -f FASTA_FILE, --fasta-file FASTA_FILE
                                Assembly scaffolds\contigs or full genomes
          -c CONFIG, --config CONFIG
                                config file
          -v, --verbose
          -t THREADS, --threads THREADS
                                num of threads (default is num of CPUs)
          -o, --output OUTPUT 
                                output filename for html and txt outputs. Required by default, but not required for stdout only output
          -p, --print-vogs
                                print phage vogs for each region
          --no-html 
                                do not generate output html file
          --not-open 
                                do not open automatically html file
          -e, --extension
                                type of the output: html, txt or stdout. Default is html. You can specify several file formats with a space as a separator. Example: -e txt html stdout
          --not-open
                                do not open html file automatically, if html output type is specified
        ```
        Running time depends on the size of your input data and the number of CPUs used.
        The approximate running time for a metagenomic assembly file of 150MB is about 20 minutes.
        
        ## Output
        The output can be on html, text or stdout format.
        
        ## Modus operandi
        ORFs and corresponging proteins are predicted from the input .fasta file using Prodigal. 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, adress estarikova@rcpcm.org
        
        (c) E.Starikova, P. Tikhonova, N.Pryanichnikov, 2019
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
