emodpy_malaria.serialization.replace_genomes module#

class emodpy_malaria.serialization.replace_genomes.Genome[source]#

Bases: object

Represent a single genome

convert_char_to_int()[source]#
create_genome(allele_root_id)[source]#
property barcode#
property hashcode#
set_allele_roots(root)[source]#
to_dtk_dict()[source]#
to_dtk_map_entry()[source]#
emodpy_malaria.serialization.replace_genomes.print_hashcodes(ser_pop)[source]#
emodpy_malaria.serialization.replace_genomes.get_next_genome(next_barcode_fn, allele_root_id, ser_pop_genome_map, cache_genome_map)[source]#
emodpy_malaria.serialization.replace_genomes.replace_genomes(input_file, next_barcode_fn, output_file)[source]#

Replaces genomes in infected individuals and vectors.

Parameters:

  • input_file – Input serialized population file

  • next_barcode_fn – Function that return the next barcode. The function is called once for every infection of an individual and once for every vector in the vector population.

  • output_file – Output file with replaced genomes.

Returns:

Nothing

emodpy_malaria.serialization.replace_genomes.test_replace_genomes(input_fn, get_next_barcode)[source]#