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View gpu.json
{
"__default__" :
{
"time" : "0-04:00:00",
"n" : 1,
"account" : "kernlab",
"partition" : "kerngpu",
"mem" : "3G",
"cores" : "1",
"chdir": "/gpfs/projects/kernlab/vsb/projects/bprime/msprime/",
View sparklines.py
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
vsbuffalo / lifeweeks.py
Created Feb 22, 2021
your life, visualized in weeks
View lifeweeks.py
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)
View simple.slim
initialize() {
initializeMutationRate(1e-8);
initializeMutationType("m1", 0.5, "f", 0.0);
initializeGenomicElementType("g1", m1, 1);
initializeGenomicElement(g1, 0, 99999);
initializeRecombinationRate(1e-8);
}
1 early() {
View fix_spines.py
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()
View Snakefile
import numpy as np
np.random.seed(1)
DATADIR = "sim_results/"
SLIM = "/home/vsb/src/SLiM_build/slim "
## Parameters
nreps = range(50)
# ------- Shared Parameters -------
View Snakefile
import numpy as np
np.random.seed(1)
DATADIR = "sim_results/"
SLIM = "/home/vsb/src/SLiM_build/slim "
## Parameters
nreps = range(50)
# ------- Shared Parameters -------
View Snakefile
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)
View split.slim
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
vsbuffalo / pairwise_cov.r
Created Mar 1, 2019
comparing two implementations of covariance with pairwise complete cases
View pairwise_cov.r
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