{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import os\n",
    "from Bio.PopGen import SimCoal as simcoal\n",
    "from Bio.PopGen.SimCoal.Template import generate_simcoal_from_template\n",
    "from Bio.PopGen.SimCoal.Controller import FastSimCoalController as fsc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/tra/anaconda3/envs/book2/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data\n",
      "['decline_split.par', 'split_ssm_2d.par', 'island.par', 'ssm_1d.par', 'ssm_2d.par', 'split_island.par', 'simple.par', 'decline_lambda.par', 'bottle.par', 'split_ssm_1d.par']\n"
     ]
    }
   ],
   "source": [
    "print(simcoal.builtin_tpl_dir)\n",
    "print(os.listdir(simcoal.builtin_tpl_dir))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['//Parameters for the coalescence simulation program : simcoal.exe\\r\\n', '1 samples\\r\\n', '//Population effective sizes (number of genes 2*diploids)\\r\\n', '?pop_size\\r\\n', '//Samples sizes (number of genes 2*diploids)\\r\\n', '?sample_size\\r\\n', '//Growth rates\\t: negative growth implies population expansion\\r\\n', '0\\r\\n', '//Number of migration matrices : 0 implies no migration between demes\\r\\n', '0\\r\\n', '//historical event: time, source, sink, migrants, new deme size, new growth rate, migration matrix index\\r\\n', '0 historical events\\r\\n']\n"
     ]
    }
   ],
   "source": [
    "f = open(simcoal.builtin_tpl_dir + os.sep + 'simple.par')\n",
    "print(f.readlines())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Genome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "n_indep_MSATs = [(200, [('MICROSAT', [1, 0, 0.005, 0, 0])])]  # refer fastsimcoal documentation\n",
    "linked_snps = [(1, [('SNP', [200, 0.0005, 0.01])])]\n",
    "linked_DNA = [(1, [('DNA', [1000, 0.0005,  0.0000002, 0.33])])]\n",
    "complex_genome = [(2, [\n",
    "    ('DNA', [10, 0.00001, 0.00005, 0.33]),\n",
    "    ('SNP', [1, 0.001, 0.0001]),\n",
    "    ('MICROSAT', [1, 0.0, 0.001, 0.0, 0.0])])]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Demography"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "simple = [('sample_size', [30]),\n",
    "          ('pop_size', [100, 200])]\n",
    "island = [('sample_size', [30]),\n",
    "          ('pop_size', [100]),\n",
    "          ('mig', [0.01]),\n",
    "          ('total_demes', [10])]\n",
    "split_ssm_1d = [('sample_size', [30]),\n",
    "                ('pop_size', [100]),\n",
    "                ('mig', [0.01]),\n",
    "                ('ne', [500]),\n",
    "                ('t', [100]),\n",
    "                ('total_demes', [10])]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "generate_simcoal_from_template('island', complex_genome, island)\n",
    "generate_simcoal_from_template('simple', n_indep_MSATs, simple)\n",
    "generate_simcoal_from_template('split_ssm_1d', linked_snps, split_ssm_1d)\n",
    "#careful with overidding parameter files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Running fastsimcoal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ctrl = fsc(bin_name='fsc252')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ctrl.run_fastsimcoal('simple_100_30.par', 10)\n",
    "ctrl.run_fastsimcoal('simple_200_30.par', 10)\n",
    "ctrl.run_fastsimcoal('island_10_0.01_100_30.par', 10)\n",
    "ctrl.run_fastsimcoal('split_ssm_1d_10_100_500_0.01_100_30.par', 10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  }
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