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

linked_strs = ["742726.3.peg.2916:96, 742726.3.peg.2917:53, 742726.3.peg.2914:40, 742726.3.peg.2918:38, 742726.3.peg.2913:24, 742726.3.peg.2919:13, 742726.3.peg.2915:13, 742726.3.peg.2081:2, 742726.3.peg.204:2, 742726.3.peg.1985:2, 742726.3.peg.1976:2, 742726.3.peg.1974:2, 742726.3.peg.1944:2, 742726.3.peg.1495:2",
    "742726.3.peg.2919:167, 742726.3.peg.2918:85, 742726.3.peg.2917:47, 742726.3.peg.2914:35, 742726.3.peg.2913:29, 742726.3.peg.2916:13, 742726.3.peg.2915:12, 742726.3.peg.276:2, 742726.3.peg.275:2, 742726.3.peg.273:2, 742726.3.peg.270:2, 742726.3.peg.252:2, 742726.3.peg.2485:2, 742726.3.peg.247:2, 742726.3.peg.220:2, 742726.3.peg.2081:2, 742726.3.peg.1975:2, 742726.3.peg.1967:2, 742726.3.peg.1957:2, 742726.3.peg.1944:2, 742726.3.peg.1932:2, 742726.3.peg.170:2, 742726.3.peg.1673:2"]

# Which population to plot
species_names = ['Barnesiella_intestinihominis_62208']*len(linked_strs)


linked_genes = []
for linked_str in linked_strs:
    linked_genes.append([])
    for item in linked_str.split(","):
        subitems = item.split(":")
        gene_name = subitems[0].strip()
        count = long(subitems[1])
        if count>=10:
            linked_genes[-1].append(gene_name)
    linked_genes[-1] = set(linked_genes[-1])

# Output filename (alter as needed)
filename = parse_midas_data.analysis_directory+'Barnesiella_intestinihominis_antibiotic_gene_gain_timecourse.png'

####################################################################
#
#  Function controlling which mutations are colored
#
#      Returns: true for colored
#               false for not colored
#
####################################################################
def color_condition(population_idx, gene_name, times, gene_copynums, marker_coverages):
        
    # don't use interpolated freqs yet.    
    
    condition = (gene_name in linked_genes[population_idx])

    return condition
