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

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

// 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

/**
 * This callback will be called with the file that was dropped.
 * @callback dropCallback
 * @param file the file object
 */
/**
 * Create a file drop area
 * @param activeElement
 *          the element that the user can drop on to trigger a callback
 * @param highlightElement

keithshep

#!/usr/bin/env python -O

import argparse
import sys
import numpy
import h5py
import csv

class ColType:
    UNKNOWN = 1

keithshep

// creating a priority queue with a lambda less operator
auto pt_less = [&mat](const cv::Point& pt1, const cv::Point& pt2) -> bool {
    return mat.at<uint8_t>(pt1) < mat.at<uint8_t>(pt2);
};
priority_queue<cv::Point, vector<cv::Point>, decltype(pt_less)> erosion_candidates(pt_less);

keithshep

/**
 * A little "class" to help out with tri state checkboxes.
 */
function TriStateCheckbox(checkbox) {
    var self = this;

    var checkedVal = checkbox.prop("checked");
    var indeterminatePropName = "indeterminate";

    /**

keithshep

import requests

def main():
    exampleTaxonomy = "mmusculus_gene_ensembl"
    exampleGene = "ENSMUSG00000086981"

    urlTemplate = \
        '''http://ensembl.org/biomart/martservice?query=''' \
        '''<?xml version="1.0" encoding="UTF-8"?>''' \
        '''<!DOCTYPE Query>''' \

keithshep

import requests
import json

# a helper function that returns the error message in case there is one and
# None otherwise
def get_err_msg(x):
    if 'errorMessage' in x:
        return x['errorMessage']
    else:
        return None

keithshep

from cgi import parse_qs, escape

def application(environ, start_response):
    parameters = parse_qs(environ.get('QUERY_STRING', ''))
    if 'subject' in parameters:
        subject = escape(parameters['subject'][0])
    else:
        subject = 'World'
    start_response('200 OK', [('Content-Type', 'text/html')])
    return ['Hello %(subject)s' % {'subject': subject}]