pontikos

#!/bin/bash
#$ -S /bin/bash
#$ -o /dev/null
#$ -e /dev/null
#$ -cwd
#$ -V
#$ -R y
#$ -pe smp 1
#$ -l scr=1G
#$ -l tmem=2G,h_vmem=1G

pontikos

for f in `find /goon2/project99/IBDAJE_raw/Macrogen/ -type f -name '*_ANNO.csv' `
do
 ln -s $f csv/
done

pontikos

import sys
i=int(sys.argv[1])
d=dict()
for l in sys.stdin.readlines():
    l=l.strip().split(',')
    k=l.pop(i)
    d[k]=d.get(k,[])+l
for k in d:
    print ','.join([k]+d[k])

pontikos

import sys,gzip

vcf = gzip.open(sys.argv[1],"r")

#these 9 column headers are standard to all VCF files
STD_HEADERS=['CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT']
#the samples headers depend on the number of samples in the file
#which we find out once we read the #CHROM line
SAMPLE_HEADERS=[]

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

pontikos

seq 1 10 | xargs -I x echo number x

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

#!/bin/bash

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

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

pontikos

#Which shell?
ps | grep $$

#Which distro?
cat /etc/issue

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

pontikos

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