Vince Buffalo vsbuffalo
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| import polars as pl | |
| import numpy as np | |
| def windowed_bin(df, window_size, column, binedges, precision=5, log_precision=False): | |
| step_size = window_size | |
| def bin_values(values): | |
| bins = np.histogram(values, bins=binedges)[0] | |
| return bins.tolist() | |
vsbuffalo
/ granges.rs
Created
December 12, 2023 19:56
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| use std::{io, marker::PhantomData}; | |
| use std::io::BufRead; | |
| use coitrees::{COITree, Interval, IntervalTree}; | |
| use fnv::FnvBuildHasher; | |
| use indexmap::IndexMap; | |
| use ndarray::{Array2, Array1}; | |
| use serde::Deserialize; | |
| use thiserror::Error; | |
| use super::utils::{InputFile, FileError, BinEdges}; |
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| { | |
| "__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
/ sparklines.py
Created
June 15, 2021 22:19
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| 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 |
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| 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
/ simple.slim
Created
February 10, 2021 21:45
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| 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
/ fix_spines.py
Created
April 29, 2020 17:39
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| 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() |
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| import numpy as np | |
| np.random.seed(1) | |
| DATADIR = "sim_results/" | |
| SLIM = "/home/vsb/src/SLiM_build/slim " | |
| ## Parameters | |
| nreps = range(50) | |
| # ------- Shared Parameters ------- |
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| import numpy as np | |
| np.random.seed(1) | |
| DATADIR = "sim_results/" | |
| SLIM = "/home/vsb/src/SLiM_build/slim " | |
| ## Parameters | |
| nreps = range(50) | |
| # ------- Shared Parameters ------- |
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| 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) |
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