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

# Which population to plot 
cluster_strs = []
cluster_strs.append(["NZ_DS981457|251311", "NZ_DS981457|258660"])
cluster_strs.append(["NZ_DS981432|7433", "NZ_DS981432|9839"])
cluster_strs.append(["NZ_DS981502|14578", "NZ_DS981502|34895"])
cluster_strs.append(["NZ_DS981509|136920", "NZ_DS981509|144325", "NZ_DS981509|136920", "NZ_DS981509|153413"])
cluster_strs.append(["NZ_DS981457|217849", "NZ_DS981457|225528"])
 
clusters = []
for cluster_str_list in cluster_strs:
    snps = []
    for snp_str in cluster_str_list:
        items = snp_str.split("|")
        chromosome = items[0]
        location = long(items[1])
        snps.append((chromosome, location))
    clusters.append(set(snps))

clusters = clusters[-1:]

species_names = ["Bacteroides_coprocola_61586" for cluster in clusters]

private_prevalence_threshold = 1e-06
    
# Output filename
filename = parse_midas_data.analysis_directory+'bacteroides_coprocola_sweep_linkage_figure.png'
output_filename = parse_midas_data.analysis_directory+'bacteroides_coprocola_sweep_linkage_figure_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):
    
    condition = False 
    
    return condition
    
def color_rule_out_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths):
    
    condition = False
    
    condition = not ((chromosome,location) in clusters[population_idx])
    
    return condition
