msplotter 0.1.37

Make a graphical representation of a blastn alignment

Make a graphical representation of a blastn alignment

Multiple Sequence Plotter (MSPlotter) uses GenBank files (.gb) to align the sequences and plot the genes. MSPlotter uses the information from the CDS features section to plot the genes. To customize the colors for plotting genes, you can add a Color tag in the CDS features with color in hexadecimal. For example, add the tag /Color="#00ff00" to show a gene in green. To avoid direct manual manipulation of the GenBank file, you can edit the file with Geneious or another software and export the file with the new annotations.

MSPlotter is an easy-to-use option for people with little coding knowledge or problems running the classic app easyfig. The program offers a graphical user interface (GUI) and a command line interface (CLI).

If the user knows Python, MSPlotter uses matplotlib. Therefore, to customize your figure, the user can modify the parameters in the MakeFigure class of the msplotter module or make any necessary change in any part of the code.

I am developing MSPlotter in my free time, therefore, if you find a bug, it may take me some time to fix it, but I will try to do my best to fix the problems as soon as possible. Also, if you have any suggestions, let me know, and I will try to implement them.

Requirements

• Python 3.11 or later
• biopython 1.81 or later
• customtkinter 5.1 or later
• matplotlib 3.7 or later
• blastn must be installed locally and in the path

MSPlotter has been tested in macOS and Windows.

Installation

First, create a virtual environment with conda or venv. Then, install msplotter using pip as follows:

pip install msplotter

Usage and options

To run the GUI type:

msplotter --gui

Output GUI:

To view all the options run:

msplotter --help

Partial output CLI:

usage: msplotter [-h] [-v] [-i INPUT [INPUT ...]] [-o OUTPUT] [-n NAME] [-f FORMAT] [-d DPI]
                 [--alignments_position ALIGNMENTS_POSITION] [--identity_color IDENTITY_COLOR]
                 [--annotate_sequences [ANNOTATE_SEQUENCES]] [--annotate_genes [ANNOTATE_GENES]] [-g]

Make a graphical representation of a blastn alignment.

Help:
  -h, --help            Show this help message and exit.
  -v, --version         Show program's version number and exit

Required:
  -i INPUT [INPUT ...], --input INPUT [INPUT ...]
                        Path to input files. Provided files must be GenBank files.

Optional:
  -o OUTPUT, --output OUTPUT
                        Path to output folder.
                        Default: current working directory.
  -n NAME, --name NAME  Name of figure.
                        Default: `figure`.
  -f FORMAT, --format FORMAT
                        Format of figure. Options: pdf, png, and svg.
                        For a complete list of valid options visit:
                        https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
                        Default: `png`.
  -d DPI, --dpi DPI     Resolution in dots per inch.
                        Default: 300 (high resolution for print).
  --alignments_position ALIGNMENTS_POSITION

Usage examples CLI

To make a figure with default parameters:

msplotter -i path/file_1.gb path/file_2.gb path/file_3.gb

To save a figure in pdf format:

msplotter -i path/file_1.gb path/file_2.gb path/file_3.gb -f pdf

Notes

I started this project to make a figure paper with three sequences with lengths between 8 to 23 kb. However, the matplotlib parameters can be adjusted for larger, smaller, or more sequences.

Credits

Inspired by easyfig: Sullivan et al (2011) Bioinformatics 27(7):1009-1010

License

BSD 3-Clause License