README.md

EasyFig 3 - version 3.2.1

Easyfig 3 is a tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recoding of Easyfig 2 initially developped by Mitchell J. Sullivan [https://mjsull.github.io/Easyfig/]

Authors: LECLERCQ Sébastien - BRANGER Maxime

Licence

Creative Commons Attribution-ShareAlike 4.0 International

CC BY-SA 4.0

Installation

On Linux/MacOS

Conda

conda env create -f requirements.yml
./Easyfig

You can also add 'Easyfig' to your PATH.

On Windows

Conda

open an anaconda powersheel terminal, then run this (can take a while) :

conda env create -f requirements_windows.yml
conda activate easyfig
pip3 install cairosvg
conda deactivate  

To launch Easyfig 3, you need to open an anaconda powersheel terminal, then

conda activate easyfig
python Easyfig.py
conda deactivate  

These steps can be done in an executable .bat file.

Blast is not included in the conda environment for Windows.
You need to install it on your own : [https://www.ncbi.nlm.nih.gov/books/NBK52637] (NCBI)
Please pay attention to the Configuration section of NCBI tutorial to correctly configure your installation.
blast executables must be in your env PATH.

Interface

General

General settings are prposed on top of the application.

You can manually set the figure output width (the height is automatically determined by the number of sequences to print).
Left/right/top/bottom margins can also manually be determined independently.

The output figure path and name can be set by clicking on the Draw figure in icon.

The CREATE FIGURE button generates the figure in SVG or PNG format. If no figure path and name is set when pressing it, a prompt window will ask you to.

See Descriptions options for more information

Saving/Loading

By clicking on the Application menu, you will be able to save your current project (every sequences and fields) with Save/Save as..., or only the configuration (features, blast, legends and decorum) with Save configuration. You will also be able to load previous saved projects with Open or configuration files with Load configuration. Loading a configuration file will keep already imported sequences and apply the saved feature/legend/decorum/blast configuration on them.

Status bar

Information about actions is displayed in the status bar at the bottom of the application. Standard information are in black, while it turns in green when the figure was successfully created or in red when an error occurred.

Sequences panel

This panel provides all parameters for each imported sequence. The General line defines default values that will be used if no specific parameter is set for a sequence (i.e. when '-' is set in a field).

Sequences in fasta or GenBank formats can be imported using the + icon. Only nucleotide/genomic sequences are accepted. Multi-fasta or -Genbank are accepted ; each internal sequence will be imported as an independent sequence. The sequence name is equal to the LOCUS field in the GenBank file and cannot be modified in Easyfig 3. Sequence identification displayed in the figure can be changed using the label type field (species, description, size,...).

GenBank sequence information is provided by clicking on the infos icon. If any information (except the LOCUS field) is modified in GenBank files while EasyFig is running, the file must be loaded again using the reload button from the sequence information pop-up.

Sequences can be deleted using the cross icon on the left of the sequence name. Beware, there is currently no warning for sequence deletion !

You can enable/disable a sequence drawing with the active field. Sequence ordering can be changed by dragging up and down the sequence name.

Vertical space between sequences can be changed using the space below field.

See Descriptions options for information on each field

Features panel

This panel will help you to display the features included in the GenBank annotation. You can add as many as you want using the + icon. Like sequences, the General line defines common parameters if no specific value is set up for a feature's field. You can choose to display or not a feature with the selected field.

Feature definitions can be deleted or copied using the cross and copy icons on the left of the feature name.