<?xml version="1.0" encoding="utf-8" ?><rss version="2.0"><channel><title><![CDATA[somebody oneday]]></title><description><![CDATA[我不想停下]]></description><link>https://blog.youkuaiyun.com/baker00</link><language>zh-cn</language><generator>https://blog.youkuaiyun.com/</generator><copyright><![CDATA[Copyright &copy; baker00]]></copyright><item><title><![CDATA[将 paired count 和unpaired count 相加]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/48132363</link><guid>https://blog.youkuaiyun.com/baker00/article/details/48132363</guid><author>baker00</author><pubDate>Mon, 31 Aug 2015 13:02:59 +0800</pubDate><description><![CDATA[尝试 count-based 算表达量过后，因为在map这一步一直是把过滤过后的paired 和unpaired reads 一起做的，后面count的时候就要出问题。发现可以用 samtools 从 bam 里分出来，于是就分开count，最后把reads 数相加。在用DESeq什么的。
首先，记下 samtools 命令
samtools view -bf  -1 all.bam > pa]]></description><category></category></item><item><title><![CDATA[python 提取文件指定列]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/48010961</link><guid>https://blog.youkuaiyun.com/baker00/article/details/48010961</guid><author>baker00</author><pubDate>Wed, 26 Aug 2015 21:53:37 +0800</pubDate><description><![CDATA[之前用featureCount 处理得到结果，要提出第一列gene_id 和 readcount 列，首先软件输出的第一行默认是你使用的命令行，没有用，用bash批量删掉。
for i in `ls`;do sed -i '1d' $i;done
删除当前文件夹下所有文件第一行。
其实提出两列很简单，不过我受够了每次一个文件执行一次的烦。想搞成别的程序调用时命令行参数直接就行。第一次知道sy]]></description><category></category></item><item><title><![CDATA[超算上安装python+HTSeq+numpy+easy_install]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47975619</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47975619</guid><author>baker00</author><pubDate>Tue, 25 Aug 2015 13:47:34 +0800</pubDate><description><![CDATA[之前用tophat+cufflinks 算了RNA-seq差异表达，想用DESeq试下。查的protocol是要用HTSeq处理map的结果，也就是count reads。但是HTSeq是一个python的包，需要numpy，没有root权限，半天搞不好。记录下：
1.下载HTSeq
下载

传到主机上，python setup.py build 出错。
2.直接非root权限安装一个p]]></description><category></category></item><item><title><![CDATA[统计个数]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47808465</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47808465</guid><author>baker00</author><pubDate>Thu, 20 Aug 2015 15:34:21 +0800</pubDate><description><![CDATA[in 文件每行有三列，tab分隔，统计最后一列每个字符出现的字数，其实是数字，但是当作字符处理。没什么问题，主要是最后想要对dict 按key值排序出了问题，python3 的dict不能用sort 什么的，最后也只能搞成按字符排序，而不是按key的数值排序。
摘抄一段python 文档

>>> # regular unsorted dictionary
>>> d = {'banana']]></description><category></category></item><item><title><![CDATA[Counting Point Mutations]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47789877</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47789877</guid><author>baker00</author><pubDate>Wed, 19 Aug 2015 22:43:19 +0800</pubDate><description><![CDATA[Problem



Figure 2. The Hamming distance between these two strings is 7. Mismatched symbols are colored red.


Given two strings  and  of
 equal length, the Hamming
 distance between  and ,]]></description><category></category></item><item><title><![CDATA[vi的复制粘贴命令]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47375295</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47375295</guid><author>baker00</author><pubDate>Sun, 09 Aug 2015 13:29:06 +0800</pubDate><description><![CDATA[vi编辑器有3种模式：命令模式、输入模式、末行模式。掌握这三种模式十分重要：

　　命令模式：vi启动后默认进入的是命令模式，从这个模式使用命令可以切换到另外两种模式，同时无论在任何模式下只要按一下[Esc]键都可以返回命令模式。在命令模式中输入字幕“i”就可以进入vi的输入模式编辑文件。

　　输入模式：在这个模式中我们可以编辑、修改、输入等编辑工作，在编辑器最后一行显示一个“--INS]]></description><category></category></item><item><title><![CDATA[Computing GC Content]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47348911</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47348911</guid><author>baker00</author><pubDate>Sat, 08 Aug 2015 00:32:47 +0800</pubDate><description><![CDATA[Problem

The GC-content of a DNA string is given by the percentage of symbols in
 the string that are 'C' or 'G'. For example, the GC-content of "AGCTATAG" is 37.5%. Note that the reverse
 complem]]></description><category></category></item><item><title><![CDATA[Rabbits and Recurrence Relations]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47122043</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47122043</guid><author>baker00</author><pubDate>Wed, 29 Jul 2015 09:27:59 +0800</pubDate><description><![CDATA[Problem

A sequence is an ordered collection of objects (usually numbers), which are
 allowed to repeat. Sequences can be finite or infinite. Two examples are the finite sequence (π,−2√,0,π) and
 ]]></description><category></category></item><item><title><![CDATA[树莓派 raspberry安全关机命令重启命令]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47108511</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47108511</guid><author>baker00</author><pubDate>Tue, 28 Jul 2015 17:23:19 +0800</pubDate><description><![CDATA[树莓派可以通过下面几个命令来实现安全关机：
sudo shutdown -h now
sudo halt
sudo poweroff
sudo init 0

上面四行代码都可以，执行一行都可以安全关机, ^_^

树莓派重启 定时重启方法：
sudo reboot
shutdown -r now
shutdown -r 04:00:00 #定时重启在凌晨四点关闭重启]]></description><category></category></item><item><title><![CDATA[Raspberry vnc 连接]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47100617</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47100617</guid><author>baker00</author><pubDate>Tue, 28 Jul 2015 16:47:25 +0800</pubDate><description><![CDATA[型号：B型
红底的板子应该是国产的。
芯片：BCM2835
USB扩展：2
储存卡：SD卡
GPIO：26
内存：512M


之前在学校，通过交换器连上，ssh连接上装了系统。一直不知道怎么让树莓派连上互联网，然后安装软件因为学校的网需要认证。
家里笔记本用无线了，
需要：一根网线，笔记本，树莓派
软件：putty，tightvnc
第一步：笔记本连上无线，用网线将笔记]]></description><category></category></item><item><title><![CDATA[Complementing a Strand of DNA]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47087447</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47087447</guid><author>baker00</author><pubDate>Mon, 27 Jul 2015 17:06:56 +0800</pubDate><description><![CDATA[Problem

In DNA strings, symbols 'A'
 and 'T' are complements of each other, as are 'C' and 'G'.

The reverse
 complement of a DNA string  is
 the string  formed
 by reversing the symbols of ,]]></description><category></category></item><item><title><![CDATA[17个新手常见Python运行时错误]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/47087189</link><guid>https://blog.youkuaiyun.com/baker00/article/details/47087189</guid><author>baker00</author><pubDate>Mon, 27 Jul 2015 16:45:37 +0800</pubDate><description><![CDATA[当初学 Python 时，想要弄懂 Python 的错误信息的含义可能有点复杂。这里列出了常见的的一些让你程序 crash 的运行时错误。

1）忘记在 if , elif , else , for , while , class ,def 声明末尾添加
 ：（导致 “SyntaxError ：invalid syntax”）

该错误将发生在类似如下代码中：



?

]]></description><category></category></item><item><title><![CDATA[Transcribing DNA into RNA]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/46992217</link><guid>https://blog.youkuaiyun.com/baker00/article/details/46992217</guid><author>baker00</author><pubDate>Tue, 21 Jul 2015 21:16:02 +0800</pubDate><description><![CDATA[Transcribing DNA into RNA

第二题也很简单，不过python还是有很多细节要注意。比如string 是不可变数据类型，可见转载17个新手常见Python运行时错误

file=open('rosalind_rna.txt','r');
seq=file.read();
leng=len(seq);
for i in range(0,leng):
    if se]]></description><category></category></item><item><title><![CDATA[Counting DNA Nucleotides]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/46827769</link><guid>https://blog.youkuaiyun.com/baker00/article/details/46827769</guid><author>baker00</author><pubDate>Fri, 10 Jul 2015 10:50:21 +0800</pubDate><description><![CDATA[第一题很简单，但是没怎么用过python，一道题中还是学到很多。counting DNA nucleotide
dna=open('rosalind_dna.txt','r');
这只是一个句柄而已，需要read（）或者 readline() 读入文件内容。
len(seq)
定义dict 还好只有4个碱基，但是以后肯定会需要更方便的定义。
d={'A':0,'C':0,'G':0,'T']]></description><category></category></item><item><title><![CDATA[codeforces #303 div2 A. Toy Cars]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/45922957</link><guid>https://blog.youkuaiyun.com/baker00/article/details/45922957</guid><author>baker00</author><pubDate>Sat, 23 May 2015 00:09:20 +0800</pubDate><description><![CDATA[A. Toy Cars


time limit per test
1 second


memory limit per test
256 megabytes


input
standard input


output
standard output



Little Susie, thanks to her older brother, likes]]></description><category></category></item><item><title><![CDATA[php实现bwt 算法]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/45699867</link><guid>https://blog.youkuaiyun.com/baker00/article/details/45699867</guid><author>baker00</author><pubDate>Wed, 13 May 2015 21:35:14 +0800</pubDate><description><![CDATA[<?php
// super Jia's implementation of the BWT
//2015年5月11日15:50:54

$string=$_POST['string1'];
$bwt_string=bwt($string);
print"oringinal string:$string";
echo"";
echo"";
print"after revert:$bwt_strin]]></description><category></category></item><item><title><![CDATA[homework2]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/44814901</link><guid>https://blog.youkuaiyun.com/baker00/article/details/44814901</guid><author>baker00</author><pubDate>Wed, 01 Apr 2015 22:14:40 +0800</pubDate><description><![CDATA[html+php+mysql使用网页对数据库的搜索和结果显示。
html 里建立表单，action属性设为php文件，input 的name属性就是提交到php中的变量名。



生物信息学homework1




search student information by ID
<form method="post"
      enctype="applicantion/x-www-fo]]></description><category></category></item><item><title><![CDATA[生信作业php连接mysql，再比对两条序列（1）]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/44521797</link><guid>https://blog.youkuaiyun.com/baker00/article/details/44521797</guid><author>baker00</author><pubDate>Sat, 21 Mar 2015 20:47:15 +0800</pubDate><description><![CDATA[生信的课后练习，发现助教留的代码很有问题，mysql插入表都有问题。 解决的第一部分是序列比对的东西，还是针对的序列本身，很简单，不过第一次用php写，贴上来。<?php
function gap_insert(&$str,$i,$length)
{
  for($j=$length;$j>$i;$j--)
	{
	 $str[$j]=$str[$j-1];
	}
  $str[$i]='-';
]]></description><category></category></item><item><title><![CDATA[527A. Playing with Paper]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/44489705</link><guid>https://blog.youkuaiyun.com/baker00/article/details/44489705</guid><author>baker00</author><pubDate>Fri, 20 Mar 2015 12:21:26 +0800</pubDate><description><![CDATA[A. Playing with Papertime limit per test2 secondsmemory limit per test256 megabytesinputstandard inputoutputstandard outputOne day Vasya was sitting on a not so interesting Maths lesson and making an]]></description><category></category></item><item><title><![CDATA[practice1的一些问题]]></title><link>https://blog.youkuaiyun.com/baker00/article/details/42389681</link><guid>https://blog.youkuaiyun.com/baker00/article/details/42389681</guid><author>baker00</author><pubDate>Sun, 04 Jan 2015 12:57:39 +0800</pubDate><description><![CDATA[这次的数据处理，在开始之前就遇到不少问题。现在记录下来：
首先是装几个软件，samtools需要make一下，但是都说是make一下，怎么是make一下呢。就是解压后，cd进入samtools文件夹，没有samtools这个可执行文件，然后输入make samtools 就这样。可能我比较脑残，弄了10多分钟才想出来。
然后把samtools ,bowtie, bowtie-build, bo]]></description><category></category></item></channel></rss>