EAGLE - Essential and Advantageous Genes Location Explorer

Now it works only for bacterial genomes

Requirements

MUSCLE
MAFFT
MSAProbs
HMMER3
EMBOSS + PHYLIPNEW (EMBASSY package)
FastME 2.07
Blast+
KaKs_Calculator 2.0
Python 2.7

Python packages:

  - wget >= 3.2
  - pyaml >= 3.12
  - numpy >= 1.14.3
  - pandas == 0.22.0
  - matplotlib >= 2.2.3
  - scipy >= 1.1.0
  - DendroPy >= 4.4.0
  - biopython >= 1.72
  - redis >= 2.10.6
  - psutil >= 5.6.1

How to use

Pull the docker image

docker pull loven7doo/eagle

The workdir in this image is '/EAGLE' so to run all commands from the image use this way:

docker run -v </host/system/workdr/location/>:/EAGLE <any command>

Do not forget to replace the path to the host system workdir with '/EAGLE' in commands

If docker is not the appropriate way follow steps below (requirements installation and the package installation)

Instal the requirements

It can be very difficult to install some requirements on Windows. Linux is recommended to use.

Install the package:

pip install git+https://github.com/loven-doo/EAGLE.git --upgrade  

from dev branch:

pip install git+https://github.com/loven-doo/EAGLE.git@dev --upgrade

Prepare the database

You can (recommended way) download the default database from here. The downloaded database should be placed into the workdir (This is not usable at all - will be uprades for it. To save the diskspace, a symlink to EAGLEdb directory can be created in each workdir with 'ln -s </path/to/extracted/EAGLEdb> </path/to/workdir/EAGLEdb>' command). Each database scheme placed in <db_name>_info.json files that are located in the archive root directory ('EAGLEdb').
Other option is to build it from prepared lists of NCBI genomes:

eagle_db -dbt bacteria

The created database scheme (db_info.json) will be located in the databese directory (EAGLEdb/bacteria)

Also below is the instruction for building a database from NCBI if you do not like to use the default database or prepared lists (another option):

1. Download assembly summary (here is RefSeq assembly summary table for bacteria and here is Genbank assembly summary table for bacteria).

2. Prepare genomes lists:

eagle_db.prepare_ncbi_summary <downloaded/summary/path> <prepared/genomes/list/path>

3. Build the database

eagle_db -dbt bacteria -igenbank <prepared/genomes/list/path>

All this commands can be run as Python functions: see below eagledb package reference

Run the analysis

WARNING: sequences names in input fasta file longer than 10 symbols may produce errors.

Type the command below to start the analysis:

eagle -i <fasta/path> -db <EAGLEdb/scheme/json/path> -nt <threads_number> -o <out/dir/path>

for detailed parameters description type:

eagle -h

Also the analysis can be run from Python:

from eagle import explore_orfs

explore_orfs(...)

Packages reference

eagle

eagledb