vsbuffalo

{
    "__default__" :
    {
        "time" : "0-04:00:00",
        "n" : 1,
        "account" : "kernlab",
        "partition" : "kerngpu",
        "mem" : "3G",
        "cores" : "1",
        "chdir": "/gpfs/projects/kernlab/vsb/projects/bprime/msprime/",

vsbuffalo

import operator
from collections import defaultdict

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib.collections import PatchCollection, LineCollection
from matplotlib.patches import Rectangle
import matplotlib.patches as mpatches

vsbuffalo

from datetime import date, timedelta
import math
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
from matplotlib.collections import PatchCollection

mean_le = math.ceil(78.54) # for men in US
birthday = (1986, 12, 19)
deathday = (mean_le + birthday[0], 12, 19)

vsbuffalo

initialize() {
  initializeMutationRate(1e-8);
  initializeMutationType("m1", 0.5, "f", 0.0);
  initializeGenomicElementType("g1", m1, 1);
  initializeGenomicElement(g1, 0, 99999);
  initializeRecombinationRate(1e-8);
}


1 early() {

vsbuffalo

def fix_spines(ax, connect=True, x=True):
    """
    Beautifies spines by stopping them at the last tick mark. If connect=False,
    also stops them at the first tick mark. For y-axis only, set x=False.
    """
    ylim = ax.get_ylim()
    xlim = ax.get_xlim()
    yticks = ax.get_yticks()
    xticks = ax.get_xticks()

vsbuffalo

import numpy as np
np.random.seed(1)

DATADIR = "sim_results/"
SLIM = "/home/vsb/src/SLiM_build/slim "

## Parameters
nreps = range(50)

# ------- Shared Parameters -------

vsbuffalo

import numpy as np
np.random.seed(1)

DATADIR = "sim_results/"
SLIM = "/home/vsb/src/SLiM_build/slim "

## Parameters
nreps = range(50)

# ------- Shared Parameters -------

vsbuffalo

import numpy as np
import slper.slimfile as sf
np.random.seed(1)

DATADIR = "../data/sims/"
SLIM = "/home/vsb/src/SLiM_build/slim "

## Parameters
nreps = range(50)

vsbuffalo

initialize() {
  defineConstant('tmu', 1e-8);
  defineConstant('nmu', 1e-8);
  defineConstant('rbp', 1e-8);
  defineConstant('N', 1000);
  defineConstant('alpha', 0.01);
  defineConstant('nrep', 1);
      
  defineConstant("seed", getSeed());
  defineConstant("data_dir", '../data/sims/');

vsbuffalo

library(tidyverse)
library(MASS)

pcov <- function(x) {
  xs <- scale(x, scale=FALSE)
  dd <- as.integer(!is.na(x))
  dim(dd)  <- dim(x)
  denom <- (t(dd) %*% dd) - 1L
  no_obs <- denom == 0L
  xs[is.na(xs)] <- 0