{ "info": { "author": "E.Starikova, N.Pryanichnikov, P.Tikhonova", "author_email": "hed.robin@gmail.com", "bugtrack_url": null, "classifiers": [], "description": "# Phigaro v 0.2.1.8\nPhigaro is a command-line tool for predicting and annotating phages and prophages from nucleid acid sequences (including metagenome assemblies) and is based on identifying phage genes via pVOG profile HMMs and a smoothing window algorithm. https://doi.org/10.1101/598243\n\n## Requirements\nIn order to run Phigaro, you need to have Prodigal and HMMER installed.\nTo install Prodigal, download it at https://github.com/hyattpd/Prodigal/wiki/installation and follow the instructions.\nTo install HMMER, download it at http://hmmer.org/.\nYou also need `locate`. It is pre-installed in the latest Ubuntu distributions, but in case you don't have it, please run `sudo apt-get install locate`.\n\n## Installation\n\n```\nsudo -H pip3 install phigaro\n```\nthen create a config file with:\n```\nphigaro-setup\n```\nIt may take some time, since you are downloading the databases.\n\n## Permissions\nBy default, root permissions are required for the installation. But you can disable it by adding a flag to '''phigaro-setup''':\n```\nphigaro-setup --no-updatedb\n```\nMoreover, you may want to change a path of a config installation file r reconfigurate ypur Phigaro - these can be also done by adding special flags:\n```\nphigaro-setup --help\nusage: phigaro-setup [-h] [-c CONFIG] [-p PVOG] [-f] [--no-updatedb]\n\nPhigaro setup helper\n\noptional arguments:\n -h, --help show this help message and exit\n -c CONFIG, --config CONFIG\n Path to a config.yml, default is\n /home/polly/.phigaro/config.yml (default:\n /home/polly/.phigaro/config.yml)\n -p PVOG, --pvog PVOG pvogs directory, default is /home/polly/.phigaro/pvog\n (default: /home/polly/.phigaro/pvog)\n -f, --force Force configuration and rewrite config.yml if exists\n (default: False)\n --no-updatedb Do not run sudo updatedb (default: False)\n```\n\n## Usage\n\n```\nphigaro -h 15:04:32\nusage: phigaro [-h] [-V] -f FASTA_FILE [-c CONFIG] [-p] [-e EXTENSION [EXTENSION ...]] [-o OUTPUT] [--not-open] [-t THREADS]\n\noptional arguments:\n -h, --help show this help message and exit\n -f FASTA_FILE, --fasta-file FASTA_FILE\n Assembly scaffolds\\contigs or full genomes\n -c CONFIG, --config CONFIG\n config file\n -v, --verbose\n -t THREADS, --threads THREADS\n num of threads (default is num of CPUs)\n -o, --output OUTPUT \n output filename for html and txt outputs. Required by default, but not required for stdout only output\n -p, --print-vogs\n print phage vogs for each region\n --no-html \n do not generate output html file\n --not-open \n do not open automatically html file\n -e, --extension\n 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\n --not-open\n do not open html file automatically, if html output type is specified\n```\nRunning time depends on the size of your input data and the number of CPUs used.\nThe running time for a metagenomic assembly file of 150MB is about 20 minutes.\n\n## Output\nThe output can be annotated prophage genome maps (html) or tabular format (text or stdout).\n\n## Test data\nTest data is available in `test_data` folder. \nIn order to run Phigaro on test data, enter the following command from your Phigaro folder:\n\n```\nphigaro -f test_data/Bacillus_anthracis_str_ames.fna -o test_data/Bacillus_anthracis_str_ames.phg -p --not-open\n```\nThis command generates `Bacillus_anthracis_str_ames.phg` and `Bacillus_anthracis_str_ames.phg.html` files in `test_data` folder.\nIf output file is not specified with `-o`, the following output is generated:\n```\nscaffold begin end taxonomy\nNC_003997.3 451613 457261 Siphoviridae\nNC_003997.3 460328 482139 Siphoviridae\nNC_003997.3 3460450 3482979 Siphoviridae\nNC_003997.3 3495703 3505502 Siphoviridae\nNC_003997.3 3749518 3776811 Siphoviridae\nNC_003997.3 3779698 3784171 Siphoviridae\n```\n\n## Methods overview\nOpen-reading frames (i.e. proteins) are predicted from the input FASTA file using Prodigal. Phage genes are annotated with prokaryotic viral orthologous groups (pVOGs) profile Hidden Markov Models (HMMs), which 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 (a triangular window function) determines regions with a high density of phage genes and therefore the prophage regions and boundaries, considering the pVOG annotations and the GC content.\n\n## Known issues\nPhigaro is tested on Linux systems. For MacOS, you may need to add the following softlink `ln -s /usr/libexec/locate.updatedb /usr/local/bin/updated` and run `brew install wget`. If you encounter any issues while running Phigaro on test data, please report them to us at estarikova@rcpcm.org.\n\n## Publication\nElizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Vadim M. Govorun (2019), Phigaro: high throughput prophage sequence annotation, bioRxiv 598243; doi: https://doi.org/10.1101/598243\n\n(c) E.Starikova, P. 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