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

# Which population to plot
species_names = ["Phascolarctobacterium_sp_59817"]*3
 
# Output filename
filename = parse_midas_data.analysis_directory+'Phascolarctobacterium_sp_59817_inconsistent_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
    
    final_idxs = (times==sample_time_map[parse_timecourse_data.highcoverage_end])
    antibiotic_idxs = (times==sample_time_map[parse_timecourse_data.highcoverage_antibiotic])
    
    if (final_idxs.sum() > 0) and (antibiotic_idxs.sum() > 0):

        # make sure frequency is high at final timepoint
        condition = (freqs[final_idxs]>0.3).any() 
        
        if population_idx==0:
            condition = condition and ((freqs[antibiotic_idxs]>0.9).any())
    
        elif population_idx==1:
            condition = condition and (not ((freqs[antibiotic_idxs]<0.1).any() or (freqs[antibiotic_idxs]>0.9).any()))
            #condition = condition and (gene_name=='1262914.3.peg.306')
    
        elif population_idx==2:
            # make sure frequency is not intermediate at antibiotic timepoint
            condition = condition and ((freqs[antibiotic_idxs]<0.1).any())
        
        else:
            condition=False
            
    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
