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

# Which population to plot
species_names = ["Alistipes_sp_60764"]
 
# Output filename
filename = parse_midas_data.analysis_directory+'Alistipes_sp_60764_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
    
    #if (freqs[0]<0.05) and (freqs[3]<0.05):
    #    if (freqs>0.3).any():
    #        condition=True
    
    condition = ((freqs.max()-freqs.min())>0.4)
    condition = condition and (freqs[0]<0.4) and (freqs[3]<0.4)      
    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
