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

linked_strs = ["515620.4.peg.196:212, 515620.4.rna.33:4, 515620.4.rna.55:3, 515620.4.peg.2162:3, 515620.4.peg.514:2, 515620.4.peg.2425:2, 515620.4.peg.2166:2, 515620.4.peg.1797:2, 515620.4.peg.1557:2, 515620.4.peg.1099:2"]

# Which population to plot
species_names = ['Eubacterium_eligens_61678']*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>=2:
            linked_genes[-1].append(gene_name)
    linked_genes[-1] = set(linked_genes[-1])

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