msplotter 0.1.28

Make a graphical representation of a blastn alignment

Make a graphical representation of a blantn alignment

Multiple Sequence Plotter (MSPlotter) uses GenBank files (.gb) to align the sequences and plot the genes. To plot the genes, MSPlotter uses the information from the CDS features section. To customize the colors for plotting genes, you can add a Color tag in the CDS features with a color in hexadecimal. For example, to show a gene in green add the tag /Color="#00ff00". To avoid direct the 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 uses matplotlib. Therefore, to customize your figure, you can modify the parameters in the MakeFigure class of the msplotter module.

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

Installation

Create a virtual environment and install msplotter using pip as follows:

pip install msplotter

Usage and options

To view all the options run:

msplotter --help

Output:

usage: msplotter [-h] [-v] [-i INPUT [INPUT ...]] [-o OUTPUT] [-n NAME] [-f FORMAT]
                 [--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.
                        Default: `pdf`.
  --alignments_position ALIGNMENTS_POSITION
                        Orientation of the alignments in the plot.
                        Options: `left`, `center`, and `rigth`.
                        Default: `left`.
  --identity_color IDENTITY_COLOR
                        Color map representing homology regions.
                        For a complete list of valid options visit:
                        https://matplotlib.org/stable/tutorials/colors/colormaps.html
                        Some options: `Greys`, `Purples`, `Blues`, and `Oranges`.
                        Default: `Greys`.
  --annotate_sequences [ANNOTATE_SEQUENCES]
                        Annotate sequences in the plot.
                        Options: `accession`, `name`, and `fname`.
                        `accession` and `name` are obtained from the `ACCESSION`
                        and `LOCUS` gb file tags, repectively. `fname` is the file
                        name.
                        If the flag is provided without argument, the sequences will
                        be annotated using `accession` numbers.
  --annotate_genes [ANNOTATE_GENES]
                        Annotate genes from top and bottom sequences.
                        Options: `top`, `bottom`, and `both`.
                        If the flag is provided without argument, only the genes at
                        the top of the plot will be annotated.

Graphic User Interfase:
  -g, --gui             Run app in a graphic user interface.

Usage examples

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

If you don't like the terminal and prefer a graphical user interface:

msplotter --gui

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