EasyFig 3 - version 3.2.0
Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recodong 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
./EasyfigYou can also add 'Easyfig' to your PATH.
On Windows
Conda
Blast is not include on conda environment for Windows.
You need to install it by your own : https://www.ncbi.nlm.nih.gov/books/NBK52637/
Please pay attention to the Configuration section of NCBI tutorial to correctly configure your installation.
blast executable must be in your env PATH.
conda env create -f requirements_windows.ymlTo launch Easyfig 3, you need to open an anaconda powersheel terminal, then load easyfig environment (conda activate easyfig) and finally run easyfig (python Easyfig.py).
These steps can be done in an executable .bat file.
Tutorial
- Loading sequences
- Defining some features
- Setting some decorum
- Managing legends output
- Generate your first figure
Interface
General
General settings are set on the top of the window. And you can access to more windows using tabs header.
See Descriptions options for more information
Image size
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.
Output path
The output path can be set by clicking on the dedicated icon. If it is not set while asking to "create figure", a prompt window will ask you to.
Create figure
Button to generate the figure in SVG format.
Saving/Loading
By clicking on the "Application" menu, you will be able to save your current setup (every sequences adn fields), or only the configuration (features, blas, legends except sequences). You will be also able to load previous savend project or configuration.
Sequences window
This window provides all parameters for each imported sequence.
The "General" line defines some common parameters that are used while drawing if no specific parameter is set for a sequence. (this is what a '-' means in a field)
Sequences in fasta of genbank formats can be imported using the '+' icon.
You can enable/disable a sequence draw with the active field.
See Descriptions options for more information
Features window
This window provides all parameters for features. You can set as many as you want.
Like sequences, the General line defines common parameters if a no specific value for a feature's field.
You can enable/disable a feature with the selected field. You also can display or hide a specific feature in the legend if needed.
The field "filter" can be used to select only specific features using regex syntax.
This allow you to display specific names, locus or any syntax contained in genbank file. The "in field" parameter allow to reduce the scope if needed.
See Descriptions options for more information
Blasts window
See Descriptions options for more information
Legends window
This window allows you to manage the displayed legend on the figure. By default, only the scale is printed. You can easily enable or disable each type of legend and choose where to print them out. See Descriptions options for more information
Decorum window
This window allows you to manage some additional displays on the figure, like GC%, GCskew and sequence-specific scale.
This works like sequences and features panels. You can define common parameters or enable/disable each decorum.
See Descriptions options for more information
Example of generated figure
This example shows the figure generated with the above options
Description of all options
You will find below the description for every options fields available.
General
| Option | Description | Values |
|---|---|---|
| Image width | Define the exact size of the image width. This is a fix value. | Integer |
| Figure path | Define the output file path of the figure. | - |
| Margins | Define the exact margins size of the figure. | Integer |
| Background color | Define the background color of the image. | - |
| Enhance graph | Add some shadow effects to features | Checkbox |
Sequences
| Option | Description | Values |
|---|---|---|
| Sequence name | Name of the sequence | Automatically filled by gbk/fasta sequence name |
| infos | Provide information about the sequence | - |
| active | Uncheck to not consider this sequence on drawing | Checkbox |
| height | Define th height of the sequence on the image | Integer |
| line width | Define the sequence line width | Integer |
| space below | Define the space below the current sequence | Integer |
| line color | Define the color of the sequence line | - |
| position | Determine the position of the sequence (inline) | left/right/center/best blast/custom |
| min | Position to consider to start on the sequence (default=1) | Integer |
| max | Position to consider to end on the sequence (default=max) | Integer or 'max' |
| reverse | Check to reverse the sequence | Checkbox |
| print label | Uncheck to hide sequence label | Checkbox |
| label type | Select the information to print as label | locus/species/description/locus+size/locus+species/locus+description |
| label position | Select the sequence label position | left/right/top/bottom/top-left/top-right/bottom-left/bottom-right |
| offset to seq | Offset value between sequence and label | Integer |
| label color | Select sequence label color | - |
| label size | Define sequence label size | Integer |
| print feat. label | Check to display features labels | Checkbox |
| feat. label type | Select information to print as features label | gene/product/note/locus_tag/mobile_element_type |
| feat. label position | Define features label position | top/middle/bottom |
| feat color | Define features label color | - |
| feat label size | Define features label size | Integer |
| feat label rot | Define features label rotation (default=0) | Integer |
Features
| Option | Description | Values |
|---|---|---|
| selected | Allow you to select/unselect a feature for the drawing | Checkbox |
| show in legend | Determine if this feature will be show in legend | Checkbox |
| type | Select the type of feature | CDS/gene/mobile_element |
| strand | Select the strand of the feature | none/lead up/lag up |
| shape | Define the shape of the feature on the draw | arrow/rectangle/frame/signal/range/rangeL |
| hatching | Define the hatching of the feature on the draw | none/hbar/hbar2/circle/crossed/crossed2/rain/diagonal/Rdiagonal/waved/dotted/crosses |
| height ratio | Define the ratio of the feature comparing to sequence height | Float |
| fill color | Color of the feature | - |
| fill | Fill or not | Checkbox |
| line width | Line width | Integer |
| line color | Line color | - |
| filter | Using a regex to select some specific features by name/product or anything | Regex |
| in field | Fields to apply the regex filter | any/gene/product/note/mobile_element_type |
| print label | Print feature label or not | Checkbox |
| label type | Which label type to print | gene/product/note/locus_tag/mobile_element_type |
| label position | Position of the label | Opposite/top/middle/bottom |
| label color | Color of the label | - |
| label size | Size of the label | Integer |
| label rot | Rotation of the label | Integer |
Blasts
| Option | Description | Values |
|---|---|---|
| Run BlastN | - | |
| Load file | - | |
| minimum length | Integer | |
| minimum similarity | Integer | |
| minimum e-value | Float | |
| distance to sequence | Integer | |
| color (min/max) | - | |
| reversed color | Checkbox | |
| opacity | Float | |
| outline matches | Checkbox | |
| show labels | Checkbox | |
| min. match size | Integer | |
| label color | - | |
| label size | Integer | |
| decimals | Integer | |
| Matches selection | None/adjacent/All vs All/All vs one/Custom |
Legends
| Option | Description | Values |
|---|---|---|
| General display | Display/Hide this legend | Checkbox |
| Horizontal position | Select the horizontal position of the legend | left/middle/right |
| Vertical position | Select the vertical position of the legend | top/middle/bottom |
| Scaling | Define a scale ratio for this legend. (default=0.3) | Float |
| Font Size | Define the font size of the legend | Integer |
| Font color | Define the font color of the legend | - |
| Cols number | Determine the exact number of columns to use to display features legend (default=1) | Integer |
Decorum
| Option | Description | Values |
|---|---|---|
| selected | Allow you to select/unselect the decorum for the drawing | Checkbox |
| show on sequences | This button opens a popup which allows you to select/unselect sequences to print this decorum | Switches on popup |
| type | Select which type of decorum to draw | GCskew/GC%/scale |
| step | Step size in bases for calculations | Integer |
| window | Window size in bases for calculations | Integer |
| position | Position of the decorum in relation to the sequence | On sequence/above/below |
| height ratio | Define the ratio of the decorum comparing to sequence height | Float |
| line width | Line width | Integer |
| line color | Line color | - |
| reverse | Reverse min/max position | Checkbox |
| print label | Print or not the decorum label | Checkbox |
| label color | Color of the label | - |
| label size | Size of the label | Integer |
| label position | Position of the label in relation to decorum | left/right |
Logo
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