#!/usr/bin/env python
# coding: utf-8

# In[1]:


import os
from Bio.PopGen import SimCoal as simcoal
from Bio.PopGen.SimCoal.Template import generate_simcoal_from_template
from Bio.PopGen.SimCoal.Controller import FastSimCoalController as fsc


# In[2]:


print(simcoal.builtin_tpl_dir)
print(os.listdir(simcoal.builtin_tpl_dir))


# In[3]:


f = open(simcoal.builtin_tpl_dir + os.sep + 'simple.par')
print(f.readlines())


# ## Genome

# In[4]:


n_indep_MSATs = [(200, [('MICROSAT', [1, 0, 0.005, 0, 0])])]  # refer fastsimcoal documentation
linked_snps = [(1, [('SNP', [200, 0.0005, 0.01])])]
linked_DNA = [(1, [('DNA', [1000, 0.0005,  0.0000002, 0.33])])]
complex_genome = [(2, [
    ('DNA', [10, 0.00001, 0.00005, 0.33]),
    ('SNP', [1, 0.001, 0.0001]),
    ('MICROSAT', [1, 0.0, 0.001, 0.0, 0.0])])]


# ## Demography

# In[5]:


simple = [('sample_size', [30]),
          ('pop_size', [100, 200])]
island = [('sample_size', [30]),
          ('pop_size', [100]),
          ('mig', [0.01]),
          ('total_demes', [10])]
split_ssm_1d = [('sample_size', [30]),
                ('pop_size', [100]),
                ('mig', [0.01]),
                ('ne', [500]),
                ('t', [100]),
                ('total_demes', [10])]


# In[6]:


generate_simcoal_from_template('island', complex_genome, island)
generate_simcoal_from_template('simple', n_indep_MSATs, simple)
generate_simcoal_from_template('split_ssm_1d', linked_snps, split_ssm_1d)
#careful with overidding parameter files


# ## Running fastsimcoal

# In[8]:


ctrl = fsc(bin_name='fsc252')


# In[10]:


ctrl.run_fastsimcoal('simple_100_30.par', 10)
ctrl.run_fastsimcoal('simple_200_30.par', 10)
ctrl.run_fastsimcoal('island_10_0.01_100_30.par', 10)
ctrl.run_fastsimcoal('split_ssm_1d_10_100_500_0.01_100_30.par', 10)


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