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

# Which population to plot
species_names = ["Parabacteroides_merdae_56972", "Parabacteroides_distasonis_56985"] #, "Ruminococcus_torques_62045", "Faecalibacterium_prausnitzii_57453", "Faecalibacterium_prausnitzii_61481", "Bacteroides_vulgatus_57955", "Bacteroides_uniformis_57318"]
 
 
# Output filename
filename = parse_midas_data.analysis_directory+'replacement_figure.png'
output_filename = parse_midas_data.analysis_directory+'replacement_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
    
    return condition
