Esempi in Python per set_species_trait_modifiers

Esempio n. 1

File: helper_functions.py Progetto: pselvaraj87/selvaraj_vector_genetics_2020

def add_trait_modifiers(cb, transmission_to_human=0.0):

    # Add gene trait modifiers
    traits = {
        'gambiae': [{
            "Allele_Combinations": [["a0", "a1"]],
            "Trait_Modifiers": {
                "TRANSMISSION_TO_HUMAN": transmission_to_human
            }
        }, {
            "Allele_Combinations": [["a1", "a1"]],
            "Trait_Modifiers": {
                "TRANSMISSION_TO_HUMAN": transmission_to_human
            }
        }]
    }

    set_species_trait_modifiers(cb, traits)

    return {'Transmission_To_Human': transmission_to_human}

Esempio n. 2

File: single_node_no_introgression.py Progetto: pselvaraj87/selvaraj_vector_genetics_2020

def add_genes(cb):

    # Add genes
    genes = {
        'arabiensis': [{
            "Alleles": {
                "a0": 1.0
            },
            "Mutations": {}
        }],
        'funestus': [{
            "Alleles": {
                "b1": 1.0,
                "b0": 0.0
            },
            "Mutations": {
                "b1:b0": 0.0,
                "b0:b1": 0.0
            }
        }],
    }
    set_species_genes(cb, genes)

    # Add gene trait modifiers
    traits = {
        'funestus': [{
            "Allele_Combinations": [["b1", "b1"]],
            "Trait_Modifiers": {
                "MORTALITY": 100
            }
        }, {
            "Allele_Combinations": [["b0", "b0"]],
            "Trait_Modifiers": {
                "MORTALITY": 1
            }
        }]
    }
    set_species_trait_modifiers(cb, traits)

    return None

Esempio n. 3

File: single_node_gene_drive_fitness_cost.py Progetto: pselvaraj87/selvaraj_vector_genetics_2020

def add_fitness_cost(cb, mortality=1.0):

    # Add gene trait modifiers
    traits = {
        'arabiensis': [
            {
                "Allele_Combinations": [["a0", "a1"]],
                "Trait_Modifiers": {
                    "MORTALITY": mortality
                }
            },
            {
                "Allele_Combinations": [["a1", "a1"]],
                "Trait_Modifiers": {
                    "MORTALITY": mortality
                }
            },
        ]
    }
    set_species_trait_modifiers(cb, traits)

    return {'Mortality': mortality}

Esempio n. 4

File: single_node_species_introgression.py Progetto: pselvaraj87/selvaraj_vector_genetics_2020

    genes = {'arabiensis': [{
        "Alleles": {"a0": 1.0, "b0": 0.0},
        "Mutations": {"a0:b0": 0.0, "b0:a0": 0.0}
    }]
    }
    set_species_genes(cb, genes)

    # Add gene trait modifiers
    traits = {'arabiensis': [
        {
            "Allele_Combinations": [["b0", "a0"]],
            "Trait_Modifiers": {"MORTALITY": 0.9}
        },
    ]
    }
    set_species_trait_modifiers(cb, traits)

    mendelian = [
        [ModFn(DTKConfigBuilder.set_param, 'Run_Number', seed),
         ModFn(add_release, label='Mendelian', number=10000)
         ]
        for seed in range(num_seeds)
    ]

    # builder = ModBuilder.from_list(gene_drive + mendelian)
    builder = ModBuilder.from_list(mendelian)

    # Call output reporters
    # cb.add_reports(BaseVectorStatsReport(type='ReportVectorStats', stratify_by_species=1))
    cb.add_reports(BaseVectorGeneticsReport(type='ReportVectorGenetics',
                                            species='arabiensis',