ShujiaHuang

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

#1. 纯区域的Merge
sub Merge {

    my ( $dis_delta, @region) = @_; # An array , format: [chrId, start, end]

    my ( %prePos, @data, $id, $start, $end );

ShujiaHuang

# Author : Shujia Huang
# Date   : 2013-01-10

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;

my ( $posFile, $regionFile ); 

ShujiaHuang

// C++ read fa-sequence
void ReadFaSeq(const char *file, map<string, string> &fa) {

    ifstream I(file);
    if (!I){
        cerr << "Cannot open file : " << file << endl;
        exit(1);
    }

    string tmp, refId;

ShujiaHuang

"""
Test pysam
"""
import pysam
import numpy as np


def Test1 () :
    samfile = pysam.Samfile('1006-01.bam', 'rb')

ShujiaHuang

#!/usr/bin/perl

use warnings;

use strict;

use PerlIO::gzip;

die "perl $0 <.gz file in> <.gz file out>" unless @ARGV==2;

ShujiaHuang

#Author : Shujia Huang
#Date : 2010/11/27
#!/usr/bin/perl -w
use strict;

use warnings;

my ( $file, $outfile_prefix, @bin_num ) = @ARGV;
my %region2num = ( "1000upstream" => 0, "first-exon" => 1, "intron"         => 2,
				   "mid-exon"     => 3, "last-exon"  => 4, "1000downstream" => 5 );

ShujiaHuang

#!/bin/bash

# If you adapt this script for your own use, you will need to set these two variables based on your environment.
# SV_DIR is the installation directory for SVToolkit - it must be an exported environment variable.
# SV_TMPDIR is a directory for writing temp files, which may be large if you have a large data set.
#export SV_DIR=`cd .. && pwd`
SV_DIR=/home/siyang/bin/software_pip/svtoolkit
SV_TMPDIR=

runDir=

ShujiaHuang

#!/bin/sh
# Just copy and paste the lines below (all at once, it won't work line by line!)
# MAKE SURE YOU ARE HAPPY WITH WHAT IT DOES FIRST! THERE IS NO WARRANTY!
# https://gist.github.com/mxcl/1173223
function abort {
  echo "$1"
  exit 1
}

set -e

ShujiaHuang

### Read Fa sequence ###
sub ReadFaSeq {

    my ( $file, $fa ) = @_;

    my ( $refId, $seq );
    open I, $file or die "Cannot open file : $file\n";

    $/ = ">"; <I>; $/ = "\n";
    while ( <I> ) {

ShujiaHuang

### Read Fa sequence ###
sub ReadFaSeq {

    my ( $file, $fa ) = @_;

    my ( $refId, $seq );
    open I, $file or die "Cannot open file : $file\n";

    $/ = ">"; <I>; $/ = "\n";
    while ( <I> ) {