To run this script, make sure that the following files are in the same directory as the script:
peptide_data.csv: This file should contain a list of peptides and their corresponding information. The format should be the same as in the R script provided.protein_sequences.fasta: This file should contain the protein sequences that you want to analyze. The format should be the same as in a typical FASTA file.
The script first defines two functions: calculate_coverage and plot_coverage.
The calculate_coverage function takes in a Pandas DataFrame of peptides and the path to a FASTA file. The function performs the following steps:
- Loads the protein sequences from the FASTA file into a dictionary.
- Calculates the length of each protein.
- Calculates the number of peptides that cover each protein.
- Calculates the percent coverage of each protein.
- Returns a DataFrame containing the percent coverage values for each protein.
The plot_coverage function takes in a Pandas DataFrame of percent coverage values, a title for the plot, and a filename for the output file. The function creates a histogram of the percent coverage values and saves it to the specified filename.
The script then loads the peptide data from the peptide_data.csv file using the pd.read_csv function from the Pandas library. It also defines the path to the protein_sequences.fasta file.
The script calls the calculate_coverage function to calculate the proteome coverage, passing in the peptide DataFrame and the path to the FASTA file.
Finally, the script calls the plot_coverage function to plot the proteome coverage distribution and save it to a file.