rule all:
	input:
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/genomewide_selection_scan/files/annotated_all_possible_variants.txt"

rule all_possible_mutations:
	input:
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/input_files/chrM.fa",
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/input_files/haplotype_mutations.vcf"
	output:
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/genomewide_selection_scan/files/all_possible_variants_df"
	script:
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/genomewide_selection_scan/scripts/creating_all_possible_mutations_df.py"

        
rule annotate_variants:
	input:
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/genomewide_selection_scan/files/all_possible_variants_df",
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/input_files/chrM.fa",
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/input_files/haplotype_mutations.vcf",
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/input_files/Mouse_Mt_Genome_Coordinates"
	output:
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/genomewide_selection_scan/files/annotated_all_possible_variants.txt"
	script:
		"/Users/isabelserrano/Documents/Science/Analyses/Conplastic_Strains/files_and_analyses/genomewide_selection_scan/scripts/annotate_variants.py"