mbreese

#!/usr/bin/env python3
#
# Converts SIFT format files to VCF format for easier annotation lookup
# 
# Sift input gz files are tab-delimited gzip compressed files. Coordinates are 1-based, so
# this is a pretty easy conversion.
# 

import os
import sys

mbreese

db.sh

This script will manage a user-run postgres database. The main idea here is to run Postgres on a system where you don't have root access (and don't want root access). If you can not install Postgres through the system (or docker), then this is one way to still be able to use the database, even if you can't start it as a service.

1. Create a database and initialize it with a user login

   ./db.sh initdb dbname username userpass

2. Start/stop the database

mbreese

#!/home/mbreese/.local/src/bcrypt-venv/bin/python3
import sys
import bcrypt

def usage():
    sys.stderr.write('''\
Encrypting text

    Usage: bcrypt {-r} [text]
        You can also pipe raw plaintext through stdin (will be stripped unless -r is set!)

mbreese

#!/usr/bin/env python3
import os
import sys

if len(sys.argv) == 1:
    print(os.path.abspath('.'))
else:
    for arg in sys.argv[1:]:
        print(os.path.abspath(arg))

mbreese

package io.compgen.ngsutils.support;

import sun.misc.Signal;
import sun.misc.SignalHandler;

abstract public class CustomSignalHandler implements SignalHandler {

	private SignalHandler old = null;
	
	private void setOld(SignalHandler old) {

mbreese

javascript:function sendurl_to_memos(url,data){let xhr=new XMLHttpRequest();xhr.open("POST", url, true);xhr.setRequestHeader("Content-Type", "application/json");xhr.onreadystatechange=function(){if (xhr.readyState === 4) { if (xhr.status === 200) {alert("Saved!");}else{alert(xhr.readyState+"\n"+xhr.status+" error: "+this.responseText);}}};xhr.send(JSON.stringify(data));};sendurl_to_memos('$$OPENID_URL$$', {"content": document.title+"\n"+window.location.href+"\n#link"});

mbreese

#!/bin/bash
COLS="$(tput cols)"

while read LINE; do
    echo $LINE | head -c $COLS
done

mbreese

#!/bin/bash
# 
# This will by default take snapshots of all zfs filesystems, 
# but could be adapted to only pull specific ones. This script 
# will also rotate snapshots, removing those that are older 
# than 2 weeks.
#

CURDATE=$(date +%Y%m%d)
TWOWEEKSAGO=$(date -d'2 weeks ago' +%Y%m%d)

mbreese

#!/usr/bin/env python

import sys
import datetime

rate = 100000

if len(sys.argv) > 1:
    rate = int(sys.argv[1])

mbreese

#!/usr/bin/env python

import sys
import itertools

cons_key = "VEP_Consequence"
impact_key = "VEP_IMPACT"
gene_key = "VEP_SYMBOL"
csn_key = "VEP_CSN"
sift_key = "VEP_SIFT"