polyploid_setup.py

"""polyploid_setup.py
Reads the config file and instantiates all the polyploids specified.
"""

import os
import log

def make_polyploids(config):

    subfolder = config.output_folder
    polyploids=[]
    num_allos=0
    num_autos=0

    for params in  config.params_for_polyploids:
        DIV_time_MYA=params.DIV_time_MYA
        WGD_time_MYA=params.WGD_time_MYA
        divergence_distribution_parameters = params.divergence_distribution_parameters_list

        if params.name:
            species_name=params.name
        else:
            if (DIV_time_MYA==WGD_time_MYA):
                num_autos=num_autos+1
                species_name="Autopolyploid_" + str(num_autos)
            else:
                num_allos=num_allos+1
                species_name="Allopolyploid_" + str(num_allos)

        polyploid = polyploid_data(subfolder, species_name, DIV_time_MYA, WGD_time_MYA,
                                   divergence_distribution_parameters, config)
        polyploid.validate()
        polyploids.append(polyploid)

    return polyploids

class polyploid_data():

    simple_newick=""
    species_name=""
    DIV_time_MYA=0
    WGD_time_MYA=0
    FULL_time_MYA=0
    list_of_divergence_distribution_parameters = [['lognorm', 0.5, 5.27,1.0]]
    subgenome_names = ["P1", "P2"]
    original_genome_name = ["P"]
    mode="TBD"
    simulation_legs=[]
    general_sim_config=False
    species_subfolder=""      #this will be updated at run-time
    subtree_subfolder=""      #this will be updated at run-time
    analysis_step_num=1       #this will be updated at run-time
    def __init__(self, subfolder, species_name, DIV_time, WGD_time,
                 divergence_distribution_parameters_list,
                 general_sim_config):

        self.species_subfolder=os.path.join(subfolder, species_name)
        self.general_sim_config =general_sim_config
        self.DIV_time_MYA = DIV_time
        self.WGD_time_MYA = WGD_time
        self.FULL_time_MYA = general_sim_config.full_sim_time
        self.species_name = species_name
        self.list_of_divergence_distribution_parameters  = divergence_distribution_parameters_list
        #currenlty only modeling spectrum of allopolyploids
        self.mode="ALLO"
        single_simulation_leg=sim_time_interval_forward_in_time(0,
                                                                    self.FULL_time_MYA,self.subgenome_names)
        self.simulation_legs = [single_simulation_leg]

    def is_allo(self):

        if self.mode=="ALLO":
            return True
        else:
            return False


    def WGD_time_as_ks(self):

        if self.general_sim_config:
            return self.general_sim_config.Ks_per_Myr * self.WGD_time_MYA
        else:
            return False

    def DIV_time_as_ks(self):

        if self.general_sim_config:
            return self.general_sim_config.Ks_per_Myr * self.DIV_time_MYA
        else:
            return False

    def validate(self):
        full_sim_time=self.general_sim_config.full_sim_time
        if self.DIV_time_MYA > full_sim_time:
            message="DIV_time_MYA > full_sim_time. That's going to be a problem"
            log.write_to_log(message)
            raise ValueError(message)
        if self.WGD_time_MYA > full_sim_time:
            message = "WGD_time_MYA > full_sim_time. That's going to be a problem"
            log.write_to_log(message)
            raise ValueError(message)
        if self.WGD_time_MYA > self.DIV_time_MYA:
            message = "WGD_time_MYA > DIV_time_MYA. That's going to be a problem"
            log.write_to_log(message)
            raise ValueError(message)

class sim_time_interval_forward_in_time():

    interval_start_time_MY=0
    interval_end_time_MY=0
    subgenomes_during_this_interval =[]
    def __init__(self, start_time_MY, end_time_MY,subgenomes):
        self.interval_start_time_MY = start_time_MY
        self.interval_end_time_MY = end_time_MY
        self.subgenomes_during_this_interval = subgenomes

    def leg_length(self):
        return self.interval_end_time_MY-self.interval_start_time_MY