######################################################
#
# Make a copy of this file and edit it to your liking
#
######################################################

# Which population to plot
species_names = ["Bacteroides_coprocola_61586"]
 
# Output filename
filename = parse_midas_data.analysis_directory+'Bacteroides_coprocola_61586_fourgamete_timecourse.pdf'

allowed_snps = set([("NZ_DS981505", 142557), ("NZ_DS981505", 155360), ("NZ_DS981505", 155362)])

output_filename = parse_midas_data.analysis_directory+'cprocola_fourgametes_snps.txt'

####################################################################
#
#  Function controlling which mutations are colored
#
#      Returns: true for colored
#               false for not colored
#
####################################################################
def color_rule_in_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths):
    
    return (chromosome,location) in allowed_snps
    
def color_rule_out_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths):
    
    return not ((chromosome,location) in allowed_snps)
    

    
