keithshep

// forward slashes don't work well in URI components even when encoded as %2F. Many server side implementations
// still stumble on them. We can encode/decode the string with a simple scheme like:
// 'hi / there / \\ dude / \\f\\b\\\\'.replace(/\\/g, '\\b').replace(/\//g, '\\f').replace(/\\f/g, '/').replace(/\\b/g, '\\');
function encURIComp(str) {
    return encodeURIComponent(str.replace(/\\/g, '\\b').replace(/\//g, '\\f'));
}

function decURIComp(str) {
    return decodeURIComponent(str).replace(/\\f/g, '/').replace(/\\b/g, '\\');

keithshep

import csv
import requests

def build_ensembl_biomart_dict(dataset_name, key_attr, val_attr):
    # see http://ensembl.org/biomart/martview/ for the web application
    biomart_request_url_template = \
        '''http://ensembl.org/biomart/martservice?query=''' \
        '''<?xml version="1.0" encoding="UTF-8"?>''' \
        '''<!DOCTYPE Query>''' \
        '''<Query virtualSchemaName="default" formatter="CSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6">''' \

keithshep

// remove field from all samples
db.getCollection('samples').update({}, {'$unset': {'viterbi_haplotypes': 1}}, {multi: true})

// initialize fields in all samples
db.getCollection('samples').update({}, {'$set': {'viterbi_haplotypes': {}}}, {multi: true})

// how to slice without getting everything you don't care about
db.getCollection('samples').find(
    {'_id': ObjectId("55e9cf1a6606af0e6e5cb5a1")},
    {

keithshep

tmux cheat sheet

(C-x means ctrl+x, M-x means alt+x)

Prefix key

The default prefix is C-b. If you (or your muscle memory) prefer C-a, you need to add this to ~/.tmux.conf:

remap prefix to Control + a

keithshep

import itertools
import math

import numpy as np
from scipy import linalg
import matplotlib.pyplot as plt
import matplotlib as mpl
import pylab

from sklearn import mixture

keithshep

DEBUG = True
PORT = 5000
#MONGO_SERVER = 'localhost'
MONGO_SERVER = 'xyz.ppp.org'
MONGO_PORT = 27017
MONGO_DATABASE = 'xyz_db'

# the following values enumerate all possible shapes you can use for 'level_shapes' in
# the WEB_APP_CONF below
CIRCLE = "circle"

keithshep

#!/bin/sh
#
# chkconfig: 345 95 05
# description: celery daemon configured to work with the haploqa application

# If we're invoked via SysV-style runlevel scripts we need to follow the
# link from rcX.d before working out the script name.
if [[ `dirname $0` == /etc/rc*.d ]]; then
    target="$(readlink $0)"
else

keithshep

# this function echos "true" when the first argument string starts
# with the second
function startswith() {
    if [[ "${1[1, ${#2}]}" == "$2" ]]
    then
        echo 'true'
    fi
}

# scan for and process .dirconf properties files where each lines is a

keithshep

import {
    Component,
    ContentChildren,
    Input,
    QueryList,
    TemplateRef,
} from '@angular/core';

@Component({
    selector: 'pxa-tree-table',

keithshep