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

#!/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

#!/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

#!/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

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

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

library("RHmm")

sunProb <- c(0.6, 0.2, 0.15, 0.05)
cloudProb <- c(0.25, 0.25, 0.25, 0.25)
rainProb <- c(0.05, 0.10, 0.35, 0.50)
weatherDist <- distributionSet(dis="DISCRETE", proba=list(sunProb, cloudProb, rainProb), labels =c("DRY", "DRYISH", "DAMP", "SOGGY"))
weatherTransitions <- rbind(c(0.5, 0.375, 0.125), c(0.25, 0.125, 0.625), c(0.25, 0.375, 0.375))
weatherHmm <- HMMSet(initProb=c(0.63, 0.17, 0.20), transMat=weatherTransitions, distribution=weatherDist)
weatherPath <- viterbi(HMM=weatherHmm, obs=c("DRY", "DAMP", "SOGGY", "SOGGY", "DRYISH"))

keithshep

To get rid of shadows in screen captures:
defaults write com.apple.screencapture disable-shadow -bool true

To manipulate file attributes use xattr:
usage: xattr [-l] file [file ...]
       xattr -p [-l] attr_name file [file ...]
       xattr -w attr_name attr_value file [file ...]
       xattr -d attr_name file [file ...]

The first form lists the names of all xattrs on the given file(s).

keithshep

#!/bin/bash

# exit on error and don't allow the use of unset variables
set -o errexit
set -o nounset

#NOTE: you can find a list of special variables at http://tldp.org/LDP/abs/html/internalvariables.html

# quietly execute GUI applications
function quietly() {

keithshep

# grep through git history
for i in {1..20}
do
    echo "### check master~$((i - 1)) vs master~${i} diff ###"
    git diff "master~$((i - 1))" "master~${i}" | grep -i 'sample-index'
done

# merge logs across several projects
(echo "commit time,author,project,message"; \
(for i in `"ls" -d */`; do (cd $i; git log "--pretty=tformat:%ai,%an,$i,%s") 2>/dev/null; done \