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

# Which population to plot
species_names = ["Phascolarctobacterium_sp_59817"]
 
# Output filename
filename = parse_midas_data.analysis_directory+'Phascolarctobacterium_sp_59817_snp_timecourse.png'


####################################################################
#
#  Function controlling which mutations are colored
#
#      Returns: true for colored
#               false for not colored
#
####################################################################
def color_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths):
    
    condition = False
    initial_idxs = (times==sample_time_map[parse_timecourse_data.highcoverage_start_2])
    antibiotic_idxs = (times==sample_time_map[parse_timecourse_data.highcoverage_antibiotic])
    
    if (initial_idxs.sum() > 0) and (antibiotic_idxs.sum() > 0):
    
        # make sure frequency is high at final timepoint
        
        condition = ((freqs[initial_idxs]<0.5).any()) and ((freqs[antibiotic_idxs]>0.8).any())
            
    if condition:
        
        items = [chromosome, location, gene_name, variant_type]
        print_str = ", ".join([str(item) for item in items])
        sys.stderr.write("%s\n" % print_str)
    
    return condition
