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

// 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

/**
 * 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

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

#!/usr/bin/Rscript

library("animation")

# reformat a directory full of R source files
tidy.all <- function(inDir = NULL, outDir = NULL, ...) {
    if (is.null(inDir) || is.na(outDir))
        stop("inDir can't be null or NA")
    if (!file.info(inDir)$isdir)
        stop("inDir must be a directory")

keithshep

#!/bin/bash

echo "input directory: $1"
echo "output directory: $2"

for i in `ls $1` ; do echo "striping N and H calls from: $i" && egrep -v '(,N,)|(,N$)|(,H,)|(,H$)|(,n,)|(,n$)|(,h,)|(,h$)' $1/$i > $2/$i; done

keithshep

#!/usr/bin/perl
use strict;
use warnings;

my $status_output = `svn status @ARGV`;
my @split_status_lines = split(/\n/, $status_output);

foreach(@split_status_lines)
{
    if($_ =~ /^M.{5}\s+(.*)$/)

keithshep

#!/usr/bin/ruby -w

################################################################################
# Created By: Keith Sheppard (keith.sheppard@jax.org)
# Modification History:
#   July 7, 2008: Initial revision created to run the liftover utility on
#   the CGD (cgd.jax.org) imputed SNP data in comma-separated format
# 
# This is a ruby script for running liftover to map SNPs in a source
# comma-separated file to a destination file using a different NCBI genome

keithshep

# attach and detach a package:
library("MouseDivGeno")
detach(package:MouseDivGeno)

# start in 64 bit mode:
R --arch x86_64

# Stack-trace in R:
traceback()

keithshep

The liftover web app and command line download:
http://genome.ucsc.edu/cgi-bin/hgLiftOver

mapping from build # to dates and version numbers:
http://genome.ucsc.edu/FAQ/FAQreleases

chain files for converting from one build to another:
http://hgdownload.cse.ucsc.edu/downloads.html#mouse