@@ -7,118 +7,145 @@ PhageTerm.py - run as command line in a shell
VERSION
=======
Version 4.1.0 (first python3 version)
Version 4.0.0
Compatible with python 3.7
INTRODUCTION
============
PhageTerm software is a tool to determine phage termini and packaging mode
from high throughput sequences that rely on the random fragmentation of DNA (e.g.
Illumina TruSeq). Phage sequencing reads from a fastq file are aligned to the phage
reference genome in order to calculate two types of coverage values (whole genome coverage
and the starting position coverage). The starting position coverage is used to perform a
detailed termini analysis. If the user provides the host sequence, reads that does not
match the phage genome are tested on the host using the same mapping function.
PhageTermVirome software is a tool to determine phage termini and packaging mode
from high throughput sequences that rely on the random fragmentation of DNA (e.g. Covaris fragmentation)
and conservation of natural DNA ends (e.g. library preparation using Illumina TruSeq).
Phage sequencing reads from a fastq file are aligned to the assembled phage genome in order to
calculate two types of coverage values (whole genome coverage and the Starting Position Coverage (SPC)).
The starting position coverage is used to perform a detailed termini and packaging mode analysis.
If user suspect the phage to have a Mu-like type of packaging, he can additionally provide the host (bacterial)
genome sequence. This analysis will take the reads that does not match the phage genome and align them on the bacterial
genome using the same mapping function. The analysis to identify Mu-like phages is available only when providing a
single phage genome (not possible if user provide a multi-fast file with multiple assembled phage contigs).
- Multi-fasta reference e.g. VIROME
- Host : Bexare, if you are using multiple sequences, the host analysis is not possible. Separate your references if you want to do this analysis.
The previous PhageTerm program (single phage analysis) and information are still available at https://sourceforge.net/projects/phageterm/ (for versions <3.0.0)
The PhageTerm program and information is available at https://sourceforge.net/projects/phageterm/ for versions <3.0.0
and at : https://gitlab.pasteur.fr/vlegrand/ptv for versions higher.
A Galaxy wrapper version is also available at https://galaxy.pasteur.fr (for versions <3.0.0)
A Galaxy wrapper version is also available at https://galaxy.pasteur.fr (only for the first version PhageTerm, PhageTermVirome is not implemented on Galaxy yet).
Since version 3.0.0, PhageTerm can work in 2 modes:
- mono machine mode (parallelization on several cores on tne same machine).
- multi machine mode (parallelization on several machines, using intermediate files for data exchange).
- the usual mono machine mode (parallelization on several cores on the same machine).
- a new multi machine mode (advanced users) with parallelization on several machines, using intermediate files for data exchange.
The default mode is mono machine.
Version 3.0.0 up to version 4.0 work with python 2.7
Since version 4.0, PhageTerm works with python 3.7 only
Since version 4.1, pvalue and pvalue adj for peaks are printed in the workflow.txt report (case of virome analysis),
Since version 4.0, PhageTerm (now PhageTermVirome) works with python 3.7
PREREQUISITES
=============
For version 3.0 up to version 4.0 (not included)
Unix/Linux
For version 4.0
- Python 2.7.X
- matplotlib 1.3.1
- numpy 1.9.2
- pandas 0.19.1
- sklearn 0.18.1
- scipy 0.18.1
- statsmodels 0.6.1
- reportlab 3.3.0
Unix/Linux
A conda virtualenv containing python2.7 and all dependencies is provided for convenience so that users
don't need to install anything else than miniconda or conda.
- backports
- backports.functools_lru_cache
- backports_abc
- cycler
- libwebp-base
- lz4-c
- matplotlib-base
- matplotlib
- numpy
- openssl
- pandas
- patsy
- pillow
- pip
- pyparsing
- python=3.7
- python-dateutil
- python_abi
- pytz
- readline
- reportlab
- scikit-learn
- scipy
- setuptools
- singledispatch
- statsmodels
- tk
- tornado
A conda virtualenv containing python3.7 and all dependencies is provided for convenience so that users
don't need to install anything else than miniconda or conda. (See below)
For version 4.0 and higher
Unix/Linux
INSTALLING PHAGETERMVIROME USING THE CONDA VIRTUALENV (easiest option)
Then, create the miniconda environment from the PhageTerm_env.yml file for version<4.0 (python2):
You can still use the old PhageTerm under python 2.7 (but no multi-fast analysis possible) using the miniconda environment from the PhageTerm_env.yml file for version<4.0 (python2):
conda env create -f PhageTerm_env.yml
or from the PhageTerm_env_3.yml file for version >=4.0 (python3)
conda env create -f PhageTerm_env_3.yml
conda activate PhageTerm_env
Acctivate it to be able to work:
conda activate PhageTerm_env
or
conda activate PhageTerm_env_py3
COMMAND LINE
============
Basic usage with mandatory options (PhageTermVirome needs at least one read file, but user can provide a second corresponding paired-end read file if available, using the -p option).