y1000plus_tools

This code provides the scripts used to analyse protein and promoter conservation in budding yeast for [1] based on data from [2].

Getting Started

The main functions are contained in y1000_plus_tools.py

Scripts to generate analysis and figures are in the scripts folder The scripts used for ref [1] are listed in PKA_evolution_fig_notes.txt Also in the scripts folder is notebook_setup.py which you can load at the beginning of a script with:

%load notebook_setup.py

It runs the std_libraries.py file which loads all necessary libraries for the provided scripts.

A few functions from https://github.com/heineike02/yeast_esr_expression_analysis are used. They may not be necessary for your purposes and if not you can comment that import out in std_librarys.py.

Many functions require data from figshare which can be obtained from figshare https://figshare.com/articles/dataset/Paralogs_in_the_PKA_regulon_traveled_different_evolutionary_routes_to_divergent_expression_in_budding_yeast_/14428763

The following from [2] can be found at https://figshare.com/articles/dataset/Tempo_and_mode_of_genome_evolution_in_the_budding_yeast_subphylum/5854692

Folders:

	0_332yeast_genomes
	orthomcl_output 

Files:
	343taxa_speicies-name_clade-name_color-code.txt (note: This is spelled incorrectly on figshare.  I correct speicies to species in the context of these algorithms.  It is a file on its own in figshare)
	data_in_Figure2.zip -> 332_2408OGs_time-calibrated_phylogeny_species-names_updated.newick

The data should be in the following structure: y1000_plus_tools/ data/ (The .gitignore file ignores all files in this data folder) /y1000plus_tools_data /shen_2018_data /orthomcl_output
/0_332yeast_genomes /0_332yeast_assemblies /0_332yeast_genomes /332_2408OGs_time-calibrated_phylogeny_species-names_updated.newick /343taxa_speicies-name_clade-name_color-code.txt

References

[1] Heineike, B., and El-Samad, H. (2021). Paralogs in the PKA regulon traveled different evolutionary routes to divergent expression in budding yeast. Front. Fungal Biol. 2. doi:10.3389/ffunb.2021.642336.

[2] Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., et al. (2018). Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell 175, 1533-1545.e20. doi:10.1016/j.cell.2018.10.023.

Authors

• Benjamin Heineike heineike02

License

This project is licensed under the MIT License - see the LICENSE.md file for details