Develop A Script to create a bed file from Ensembl API

[limia12]

Description: Create a Python script to get gene and transcript information from the Ensembl REST API for a given species and gene symbol. The script will take details like chromosome, start and end positions, and names, and we will need this information in a BED file format.

[mm3014]

Script has been made to connect to Ensembl API and when given an input of a list of genes, to retrieve data for the chromosome that the gene is on, the genomic start position, the genomic end position and the gene name.

NEXT STEP: Code needs to be re-worked to be put into functions

[limia12]

Functioning has been added to script but needs checking to see if functions are robust enough for testing. (I have also saved a backup of the old script just in case)

NEXT STEP: Logging/ Testing

[limia12]

Meeting 22/11/2024: To do:

• [x] add chrx to bed file.
• [x] cross check format of bed file.
• [x] change parameters to reflect the official bed format. (tab delimited format)

https://genome.ucsc.edu/FAQ/FAQformat.html https://www.ensembl.org/info/website/upload/bed.html

[limia12]

26/11/2024:

I have updated the script to include chrx in the bed file, the bed file is also be in tab delimited format and the script allows for user to input their own list of genes.

I have logged the prints but we need to create a log file to store these error logs. We also need to carry out testing - I have now separated the steps into clear functions.

Next Step: Set up a meeting with Nour to intergrate our API with the panelapp API

[limia12]

27/11/2024

Meeting with Mary:

• [ ] Create a break to stop the rest of the script running if an error shows up in one of the functions.
• [ ] Also need to appropriately log each function.