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

# Which population to plot
species_names = ["Eubacterium_siraeum_57634", "Eubacterium_rectale_56927", "Barnesiella_intestinihominis_62208", "Butyrivibrio_crossotus_61674",  "Paraprevotella_clara_33712", "Alistipes_senegalensis_58364"]
 

# Output filename
filename = parse_midas_data.analysis_directory+'supplemental_example_figure_2.pdf'
stats_filename = parse_midas_data.analysis_directory+'supplemental_example_stats_figure_2.pdf'
output_filename = parse_midas_data.analysis_directory+'supplemental_example_figure_2_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
