suqingdong

#!/usr/bin/env python
#-*- encoding: utf8 -*-
import sys
import logging


class MyLogger(logging.Logger):
    def __init__(self,
                 name=None,
                 level=logging.DEBUG,

suqingdong

#!/bin/sh
part_bytes=$((1024 * 1024 * 1024))

USAGE() {
echo -e "usage: $0 [options] <url>

options:
    -o <str>  the prefix of output
    -s        run curl on silent mode
    -b <int>  the bytes of each part[default: $part_bytes]

suqingdong

问题

把snp注释结果文件按指定ROH区间输出

解决

1. 把ROH区间构建为如下结构的字典

{
  chrom: {
      (start, end): set([gene1, gene2, ...]),
 ...

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#!/bin/sh
set -eo pipefail

# *******************************************
# Script to perform DNA seq variant calling
# using a single sample with fastq files
# named 1.fastq.gz and 2.fastq.gz
# *******************************************
# Update with the fullpath location of your sample fastq
fastq_folder="/home/pipeline/samples"

suqingdong

#!/usr/bin/env python
#-*- encoding: utf8 -*-
'''\033[1;32m
    参考基因组每条染色体总长度和N的数量统计
\033[0m'''
import os
import sys
import json
import textwrap
import logging

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#!/usr/bin/env python2
# encoding: utf-8
'''\033[1;3;32m
    normalizing file with multiple encodings to utf8
\033[0m'''
import sys
import signal
import textwrap

import chardet

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# .bashrc


# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

# User specific aliases and functions
PS1="\[\e[0;35m\][\u@\h\[\e[33m\] \t \[\e[36m\]\w]\n\[\e[36m\]$\[\e[m\]"

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#!/usr/bin/env python
#-*- encoding: utf-8 -*-
import os
import argparse
import getpass
import socket
import glob

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

our $VERSION = 			'$Revision: ba2461d35c1c0732560fce2c19319479f5232d60 $';
our $LAST_CHANGED_DATE =	'$LastChangedDate: 2012-10-23 23:32:05 -0700 (Tue, 23 Oct 2012) $';

suqingdong

'''
pileup 获取指定区间reads的比对情况
       truncate=True,只输出指定位点
       stepper='samtools' 同samtools depth一样的过滤
       stepper='nofilter' 不进行任何过滤
       
fetch 抓取指定区间内的所有reads
'''

import pysam