alexpreynolds

#!/usr/bin/perl -w
use strict;

# Utility to help format my notes, progress, results etc in atomic chunks, 
# so they can be organized by project, data, technology, "todo" lists, etc.

if (@ARGV < 1) {
    die " Usage:   $0 <new | parse> \n";
    # Hidden optional arguments, not tested lately:   [tag-list or +/-days]\n";
}

alexpreynolds

p.todo { color:red; margin:0; padding:0; font-size:0.8em; }
p.done { color:green; margin:0; padding:0; font-size:0.7em; }
p.info { color:gray; margin:0; padding:0; font-size:0.8em; }
p.tags { color:gray; margin:0; padding:0; font-size:0.7em; }
p.cwd{ color:gray; margin:0; padding:0; font-size:0.8em; }
p.src { color:gray; margin:0; padding:0; font-size:0.8em; }
p.subject { color:black; margin:0; padding:0; font-size:1.5em; font-weight:bolder; }
.novel { color:green; font-weight:bolder; }
.xfac { color:#B80000; font-weight:bolder; }
.jaspar { color:#3399FF; font-weight:bolder; }

alexpreynolds

weblocal /home/areynolds/public_html
webroot /~areynolds
blogdir blog

alexpreynolds

#!/usr/bin/env python

import gzip

ASSEMBLY = "hg38"
chromosome_sizes = { "hg38" : 
    [
        {
            "name": 1,
            "size": 248956422

alexpreynolds

#!/usr/bin/env python

import sys
import math
import pandas as pd
import numpy as np
from scipy import stats
import json
from json import JSONEncoder
import zipfile

alexpreynolds

#!/usr/bin/env python                                                                                                                                                                        

import subprocess
import sys
from os import listdir
from os.path import isfile, join
import time

# image, crop dimensions                                                                                                                                                                     
img_dir = sys.argv[1]

alexpreynolds

#!/usr/bin/env python

import re
import os
import pandas as pd

in_fn = "../data/dhs_bed.bed"
column_index_to_split_on = 8
out_dir = "../results/split"

alexpreynolds

#!/usr/bin/env python

import numpy as np
from numpy.core.fromnumeric import compress
import umap
import h5py
import string
import random

'''

alexpreynolds

>42_comp5_1000_0
GAAATGGAATATTGGGTGGTAAAAGCCTGTGGTTCCCGTAGTTTAGGAGGCACAGATGGC
CTCATTACAGCCTTCAGATTCAGTACCTCAAAGAAATTTTTTTTTTTTTTGAGACAGGGT
TTCAGTTGGGAGCCACGATTGCCTAGCAAAACCACAGCACTCCATCCTGCAGGACATAGT
GAAACTGTTCTCTGAAAATA
>42_comp5_1000_1
CAGAAGTGTGGTTAGGTGGGTCATGCGTTCTATGACCTGTGCAACCAGGAAGTGAATGAC
GGTTCAGAGTGGAGACGTTCTAGAAAAATGGTACTGGCTGCTGAAGCAGGTCAGTATAAA
CATTTCAGCTACTTTGAGTGTTTCAGGAGGTGTGAAAATGACAACAGAAACTAGCTAGAG
GTGCTCAAAGATTTGGAGAA

alexpreynolds

install.packages("quantmod")
library("quantmod")
x <- seq(0, 2*pi, 0.1)
y <- sin(x)
y[findPeaks(y)]
# [1] 0.9916648
y[findPeaks(-y)]
# [1] -0.9961646