This was the first time I worked with any kind of genbank or genome data. I did not know what genome circular diagrams were either so I first searched up examples. Google provided many complicated and intricate examples, but I also found a few simpler examples that highlighted the features and their labels efficiently.
Then I researched more about how genome diagrams could be created using Python. I found a scholarly article (1) that outlines various software and libraries that are used to create genome diagrams. The article mentioned Python's GenomeDiagram (more specifically Bio.Graphics.GenomeDiagram) module from the Biopython library. With further research, I determined that I can use the GenomeDiagram module to complete the challenge.
I utilized both the GenomeDiagram documentation (2) and a tutorial on the module (3) when working to complete the challenge. The first time I created the diagram, the labels were too small and since I had only one track, several features seemed to have overlapped each other. I edited my solution to contain 2 tracks instead of 1 and implemented a color sequence that created a more appealing visualization. I also made the label size larger and positioned it to the middle. I found that there were a total of 5 gene features for the Tomato Curly Stunt Virus.
- Parveen, Alisha et al. “Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era.” Current genomics vol. 20,2 (2019): 90-99. doi:10.2174/1389202920666190314092044
- “Bio.Graphics.GenomeDiagram Package.” Bio.Graphics.GenomeDiagram Package - Biopython 1.75 Documentation, biopython.org/docs/1.75/api/Bio.Graphics.GenomeDiagram.html.
- “Graphics Including GenomeDiagram.” Graphics Including GenomeDiagram - Test Test Documentation, biopython-tutorial.readthedocs.io/en/latest/notebooks/17%20-%20Graphics%20including%20GenomeDiagram.html.