taoliu

#!/usr/bin/env bash

## pyprofile: profile Python script

## $Revision$
## Copyright 2011 Michael M. Hoffman <mmh1@uw.edu>
## Modified by Tao Liu: Correctly get the command name.

set -o nounset
set -o pipefail

taoliu

#!/bin/bash

if [[ $# < 2 ]];then
    echo 'need two parameters: $0 <interval> <pid>'
    exit 1;
fi

INTERVAL=$1
PID=$2

taoliu

#!/usr/bin/env python

import subprocess
import sys
import os
import time

#time_stamp=time.strftime("%y-%m-%d_%H-%M-%S")
time_stamp=str(time.time())

taoliu

#!/usr/bin/env python
# Time-stamp: <2012-01-10 17:21:24 Tao Liu>

# in the wiggle file from MA2C, the 1st column -- position is actually
# the center of each probe. Some probes may overlap. In order to
# convert them to appropriate bigwig, I need to create bedGraph file
# with above two problems fixed.

import os
import sys

taoliu

python -c 'import math;import random;n=1000000L;print float( n - reduce( lambda x, y: x//1+y//1, map( lambda x: math.hypot( random.random(), random.random() ), range(n) ) ) )/n*4'

taoliu

#!/bin/bash

if [ $# -lt 1 ]; then
    echo `basename $0` "<PET RNAseq SAM filename>"
    exit
fi

F=$1

# chromosome length file

taoliu

#!/usr/bin/perl -w
# Time-stamp: <2004-04-02 14:37:41 Tao Liu>

use strict;

if (@ARGV>0 and $ARGV[0] eq "-h") {
    print "ediff : compute two sets with \'or diff and\'. \nUsage:\tediff [-h] : help, this info\n\tediff A or B : union of two sets\n\tediff A diff B : elements in
 A but not in B\n\tediff A and B : intersection of two sets\n";
    exit;
}

taoliu

#!/usr/bin/env python
# Time-stamp: <2012-04-12 12:12:53 Tao Liu>

import sys
import pstats
# ------------------------------------
# Main function
# ------------------------------------
def main():
    if len(sys.argv) < 3:

taoliu

#!/bin/bash

# check commands: slopBed, bedGraphToBigWig and bedClip

which bedtools &>/dev/null || { echo "bedtools not found! Download bedTools: <http://code.google.com/p/bedtools/>"; exit 1; }
which bedGraphToBigWig &>/dev/null || { echo "bedGraphToBigWig not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }
which bedClip &>/dev/null || { echo "bedClip not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }

# end of checking

taoliu

#!/bin/bash
# modified from prockmon

unset LD_LIBRARY_PATH

if [[ $# < 2 ]];then
    echo 'Check total CPU time and maximum memory usage of a process.'
    echo 'need two parameters: $0 <interval> <pid>'
    exit 1;
fi