pontikos

testpts <- structure(list(x = c(4.9, 4.2, 4, 4.1, 4.4, 5.8, 5.8, 5.8, 5.8, 
5.5, 4.9, 3.2, 3.2, 3.3, 5.4, 5.4, 5.7, 6.4, 6.7, 6.7, 6, 4.8, 
3.6, 2.8, 3.5, 4.4, 5.1, 4, 3.7, 4.5, 4.9, 5.7), y = c(6.9, 6.2, 
5.3, 4.1, 3.1, 2.9, 2.9, 3.5, 4.2, 4.9, 5.1, 4.9, 4.9, 5.2, 6.9, 
6.9, 5.3, 3.8, 4.2, 5.6, 6.9, 5.8, 1.2, 2.5, 5.3, 6.4, 6.8, 7.6, 
6.9, 5.4, 4.8, 4.4)), .Names = c("x", "y"))
x <- do.call('cbind',testpts)
ch<-chull(x)
plot(x,pch=20)
points(x[ch,],pch=20,col='red')

pontikos

#! /bin/awk -f

BEGIN {
OFS = FS
}

{
    # only one line starting with #CHROM needs to be modified in file
    # all others just print out unmoodified
    if ( $1 !~ /^#CHROM/ ) {

pontikos

#! /usr/bin/awk -f

{
	count[$1]++
}
END {
	sort = "sort -n"
	for(j in count)
		print j, count[j] | sort
	close(sort)

pontikos

import time
import sys
print time.strftime(sys.argv[2], time.strptime(sys.stdin.read().strip(), sys.argv[1]))

pontikos

# prints to stderr in red
function error() { >&2 echo -e "\033[31m$*\033[0m"; }
function stop() { error "$*"; exit 1; }
try() { "$@" || stop "cannot $*"; }

pontikos

#Which shell?
ps | grep $$

#Which distro?
cat /etc/issue

#Which connections?
lsof -i
netstat -lptu
cat /proc/xxxx/net/tcp

pontikos

#!/bin/bash

f=$1
extension=${f##*.}

if [[ "$extension" == 'vcf' ]]
then
    in=$f
    out=${in}.gz
    bgzip $in > $out

pontikos

#! /bin/bash
set -e
set -u

##
until [ -z "$1" ]
do
    # use a case statement to test vars. we always test $1 and shift at the end of the for block.
    case $1 in
    # parameters to qsub

pontikos

seq 1 10 | xargs -I x echo number x

pontikos

for x in chr*.gvcf.gz
do
    mkdir -p ${x%%.gvcf.gz}
    ln -s `pwd`/$x.tbi `pwd`/${x%%.gvcf.gz}/Levine_test.gvcf.gz.tbi
done