GenoFig - version 1.0.5
Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recoding of Easyfig 2 initially developped by at the S. Beatson Lab [https://mjsull.github.io/Easyfig/]
Authors: LECLERCQ Sébastien - BRANGER Maxime
Table of content
- License
- Installation
- Interface
-
Description of all options
General panel
Sequences panel
Features panel
Homologies panel
Legends panel
Decorations panel
License
Copyright 2023 INRAE, Université de Tours
The GenoFig logo is trademark of INRAE, Université de Tours
Some parts of the logo are under a CC BY 3.0 license: Dna Icon Designed by vecteezy
Installation
On Linux/MacOS
Conda
Download the GenoFig source code using the 'Download' button on top of this page. Cloning is currently not available for people not member of the INRAE French Institution. After decompression, open a terminal in the folder containing the decompressed files and run:
conda env create -f requirements.yml
./SETUP.shYou can then run GenoFig with:
./GenofigYou can also add the GenoFig directory to your PATH by executing
echo 'export PATH="'$(pwd)':$PATH"' >> ~/.bashrcAfter opening a new terminal, this will allow to execute the program from any directory by simply typing 'Genofig'.
For MACOS users: You may experience mouse pointer icon weird behavior, due to system-specific implementation of GTK3 libraries. It shouldn't affect functionality.
Compiled version for MacOS
A bundled version of release 1.0.3 can be found here This version was compiled for intel-based 64 bit systems and do not work for arm64-based Apple Silicon (M1/M2/M3) systems
The bundled version does not include latest bux fixes and improvement. Note also that it takes a while to start, without any prompt (~1 min, please be patient after clicking on the icon!).
On Windows
Blast installation
On Windows, Blast is not automatically installed with GenoFig. You will need to install it on your own : Blast+ on NCBI
Please pay attention to the Configuration section of NCBI tutorial to correctly configure your installation.
blast executable must be in your env PATH.
Compiled version for Windows 10 and later
A compiled version of release 1.0.3 can be found here
Note that the compiled version takes a while to start without any prompt (~1 min., please be patient after clicking on the icon!), and does not include latest bux fixes and improvement.
Conda version
You first need to install Miniconda: Conda installation for windows.
Then, download the GenoFig source code using the Download button on top of this page and decompress it. Cloning is currently not available for people not member of the INRAE French Institution. Open an anaconda prompt (i.e. powersheel terminal), navigate to the folder containing the decompressed GenoFig code and run:
conda env create -f requirements_windows.yml
conda activate genofig
pip3 install cairosvg
conda deactivate Launch Genofig from an anaconda powersheel terminal in the directory where GenoFig was decompressed, with:
conda activate genofig
python Genofig.py
conda deactivate These steps can be inserted in an executable .bat file.
Interface
General
General settings are proposed 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 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 display settings) with Save/Save as..., or only the display settings (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 display settings on them.
Under LINUX, a specific configuration can also be saved as default, and will be automatically loaded upon GenoFig start.
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 green when the figure was successfully created or 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 plus 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 GenoFig. 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 GenoFig 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.
For MACOS users: drag-and-drop will copy the sequence instead of moving it, due to system-specific implementation of GTK3 libraries. You will need to delete the original sequence using the cross icon.
See Descriptions options for detailed 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 plus icon. Like for the Sequences panel, 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. Feature names are editable.
The most important parameter for Features is the filter field. It will help you define on which GenBank features to apply the selected parameters. For instance, defining a CDS feature with a fill color set as green and a filter set as "kinase" will print in green all CDS having the term "kinase" in any of the fields of the GenBank file. The in field field allows you to reduce the scope of the seach to a specific field of the GenBank feature (gene, product, etc.).
Values in the filter field are interpreted using regex syntax, in a case-insensitive way. This means that the OR operator '|' or metacharacters such as \d+ will work. More information on regex syntax here: https://www3.ntu.edu.sg/home/ehchua/programming/howto/Regexe.html
Features definition are interpeted from top to bottom, and only the last valid definition will be selected for each feature in the figure. For instance, a feature definition with filter set to "kinase" will never be applied if another feature definition with filter set to "kin" is present lower. Features ordering can be changed by dragging up and down the feature name.
For MACOS users: drag-and-drop will copy the feature instead of moving it, due to system-specific implementation of GTK3 libraries. You will need to delete the original feature using the cross icon.
See Descriptions options for more information
Homologies panel
Homologies between sequences can be calculated using BlastN or TBlastX. When all sequences are loaded, the Run BlastN button produces an All-vs-All blast output which needs to be saved on the disk. Blast needs to be run again only if new sequences are imported. Various parameters allow you to filter which blast hits to display from the total hits stored in the Blast file.
Homologies can be displayed between adjacent sequences, between all sequences, or all against a single sequence using the Matches selection area. Used-defined homology comparisons can also be set up using the Custom option.
The TBlastX area is hidden by default and can be displayed by clicking on the TBLASTX square button.
See Descriptions options for more information
Legends panel
This panel allows you to manage legends displayed 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. The Scaling parameter is a factor of the figure size. Blast legends use the vertical figure size while features and scale legends use the horizontal figure size. The scale is automatically reduced to the closest informative size (1Kbp, 2Kbp, 10Kbp, 20Kbp,...).
The features legend uses feature names as identifiers. Spaces are allowed, but try to avoid other special characters as much as possible.
Beware that legends are displayed in the margins of the figure. If a legend overlaps the sequences, you can enlarge the corresponding margin in the figure's General options.
See Descriptions options for more information
Decorations panel
This panel allows you to manage some additional sequence information, like GC%, GC skew or sequence-specific scales.
It works like Sequences and Features panels.
For GC% and GC skew information, the value is calculated every X nucleotides, given by the field step, on a fragment of size Y given by the window field.
For the Scale information, step and window fields represent minor and major tick bars, respectively.
By default, decorations are displayed for all sequences. They can be displayed only on some sequences by using the show on sequences icon field which will open a pop-up menu for sequence selection.
For MACOS users: drag-and-drop will copy the decoration instead of moving it, due to system-specific implementation of GTK3 libraries. You will need to delete the original decoration using the cross icon.
See Descriptions options for more information
Example of generated figure
This example shows the figure generated with the display options presented in the above example images
Description of all options
General panel
| Option | Description | Values |
|---|---|---|
| Image width | Define the exact size of the image width in pixels. Image height will be automatically computed | Integer |
| Figure path | Define the output file path for the figure. | SVG and PNG formats are supported |
| Margins | Define the top/right/bottom/left margins of the figure in pixels. | Integer |
| Background color | Define the background color of the image. | RGB color or transparent |
| Enhance graph | Add some shadow effects to features | Checkbox |
Sequences panel
| Option | Description | Values |
|---|---|---|
| Sequence name | Name of the sequence | Automatically set to the GenBank/fasta locus name |
| infos | Provide information about the sequence | - |
| active | Draw/hide the sequence | Checkbox |
| position | Determine the horizontal position of the sequence | left/right/center/best blast/custom |
| min | Start to draw the sequence at this position (default=1) | Integer |
| max | End to draw the sequence at this position (default=max) | Integer or 'max' |
| reverse | Reverse complement the sequence | Checkbox |
| height | Define the height of features on the sequence | pixel |
| space below | Define the space below the current sequence | pixel |
| line width | Define the sequence line width | pixel |
| line color | Define the color of the sequence line | - |
| seq. label | Print the sequence label | Checkbox |
| label type | Select which information to print as label. Information are extracted from the GenBank definition and may be empty for FASTA sequences | locus/accession/organism/strain/description/size or a combination |
| label position | Select the label position relative to the sequence | left/right/top/bottom or a combination |
| label offset | distance between the sequence and its label | pixel |
| label color | Sequence label color | - |
| label size | Sequence label size | pixel |
| B | Sequence label in bold | Checkbox |
| I | Sequence label in italic | Checkbox |
| feat. label | Display features labels in this sequence | Checkbox |
| feat. label type | Select which information to print as features label | gene/product/note/locus_tag/mobile_element_type |
| feat. label position | Label position relative to the features | top/middle/bottom |
| feat color | Features label color | - |
| feat label size | Features label size | pixel |
| feat label rot | Features label rotation (default=0) | angle |
Features panel
| Option | Description | Values |
|---|---|---|
| selected | activate the feature's definition | Checkbox |
| in legend | Determine if this feature will be shown in the feature legend | Checkbox |
| type | Type of the feature as defined in GenBank | CDS/gene/mobile_element/tRNA/rRNA/misc_feature |
| filter | Value to select some specific features on | Regex command |
| in field | Field on which to apply the regex filter | any/gene/product/note/mobile_element_type |
| strand | Display feature according to its strand orienttion | none/lead up/lag up |
| shape | Shape of the feature in the picture | arrow/rectangle/frame/signal/range/rangeL |
| height ratio | Size ratio of the feature compared to the sequence height value | Float |
| fill | Fill the feature with color | Checkbox |
| fill color | Filling color | - |
| line width | feature line width | pixel |
| line color | feature line color | - |
| hatching | Fill the feature with hatching, using line color and width | several choices |
| label | Print the feature label | Checkbox |
| label type | Which GenBank field to use as label | gene/product/note/locus_tag/mobile_element_type |
| label position | Label position relative to the feature | Opposite/top/middle/bottom |
| label color | Feature label color | - |
| label size | Feature label size | pixel |
| label rot | Feature label rotation | angle |
Homologies panel
Hits correspond to homologous regions detected by Blast.
| Option | Description | Values |
|---|---|---|
| Run BlastN/TBlastX | Execute blast comparisons between all sequences from the Sequence panel. Save the results in an output file | - |
| Load file | Load a previous Blast file run. Warning: only hits matching sequences (according to the LOCUS entry) from the sequence panel will be considered | - |
| minimum length | minimum hit size to display | nucleotides |
| minimum similarity | minimum hit nucleotide similarity to display | percent |
| minimum e-value | minimum hit e-value to display | Float |
| distance to sequence | distance of the beginning of the hit to the Sequence line center. | pixel |
| color (min/max) | Color gradient for balst hits display, according to min and max hit similarities | - |
| reversed color | Allow the definition of an alternative gradient for hits in reversed orientation | Checkbox |
| opacity | transparency of displayed hits | Float |
| outline matches | draw a thin outer line around hits | Checkbox |
| show labels | display hit nucleotide similarity in the center of the hit | Checkbox |
| min. match size | Minimum hit size to display the label | nucleotides |
| label color | hit label color | - |
| label size | hit label size | pixel |
| decimals | number of decimal to display | Integer |
| Matches selection | Selet between which sequences to display homologies | None/adjacent/All vs All/All vs one/Custom |
Legends panel
| Option | Description | Values |
|---|---|---|
| General display | Display/Hide this legend | Checkbox |
| Horizontal position | Horizontal position of the legend in the picture | left/middle/right |
| Vertical position | Vertical position of the legend in the picture | top/middle/bottom |
| Scaling | Scale ratio for this legend relative to the total picture size (default=0.3) | Float |
| Font Size | Font size of the legend | pixel |
| Font color | Font color of the legend | - |
| Cols number | Number of columns into which feature legends should be distributed (default=1) | Integer |
Decorations panel
| Option | Description | Values |
|---|---|---|
| selected | Show/hide the decoration when drawing | Checkbox |
| show on sequences | Select on which sequences to apply the decoration | Switches on popup |
| type | Type of decoration | GCskew/GC%/scale |
| step | GC% and GC-skew window step OR Scale minor tick interval | nucleotides |
| window | GC% and GC-skew window size OR Scale major tick interval | nucleotides |
| position | Position of the decoration relative to the sequence | On sequence/above/below |
| height ratio | Size ratio of the decoration compared to the sequence height value | Float |
| line width | Decoration line width | pixel |
| line color | Decoration line color | - |
| reverse | Reverse min/max position | Checkbox |
| print label | Print the GC%/GC-skew min max values OR positions of the scale major tick bars | Checkbox |
| label color | Decoration label color | - |
| label size | Decoration label size | pixel |
| label position | Position of the label relative to the decoration | left/right/middle |
| use original GenBank position | Display scale positions relative to the GenBank original region, when the sequence originates from a GenBank file with a REGION property (typically after downloading a subpart of a large GenBank annotated sequence) | Checkbox |