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<h2 id="A-Bioinformatician’s-UNIX-Toolbox"><a href="#A-Bioinformatician’s-UNIX-Toolbox" class="headerlink" title="A Bioinformatician’s UNIX Toolbox"></a><a href="http://lh3lh3.users.sourceforge.net/biounix.shtml" target="_blank" rel="external">A Bioinformatician’s UNIX Toolbox</a></h2><h2 id="awk、sed"><a href="#awk、sed" class="headerlink" title="awk、sed"></a>awk、sed</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div><div class="line">19</div><div class="line">20</div><div class="line">21</div></pre></td><td class="code"><pre><div class="line"># 常用</div><div class="line"># 数某一列出现次数</div><div class="line">awk '{l[$1]++}END{for (x in l) print x,l[x]}'</div><div class="line"></div><div class="line"># 去掉文件末尾的\n</div><div class="line">awk 'BEGIN{ORS=""}{print $0}' test.txt > test2.txt</div><div class="line"></div><div class="line"># RS是记录分隔符（句尾），默认的分隔符是\n</div><div class="line"># RS修改记录分隔符，ORS修改输出记录分隔符</div><div class="line"># FS指定列分隔符，OFS指定列输出分隔符</div><div class="line">awk 'BEGIN{OFS="\t"}{print $1,$2}' test1 </div><div class="line"></div><div class="line"># tar.gz</div><div class="line">.tar.gz 和 .tgz</div><div class="line">解压：tar zxf Something.tar.gz</div><div class="line">压缩：tar zcf Something.tar.gz DirName</div><div class="line"></div><div class="line">分卷压缩tar.gz: tar zcf - DirName/* |split -d -b 100m - Something.tar.gz.</div><div class="line"># 生成文件：Something.tar.gz.00 Something.tar.gz.01 Something.tar.gz.02 ...</div><div class="line">解压tar.gz分卷</div><div class="line">cat Something.tar.gz.* | tar zx</div></pre></td></tr></table></figure>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div><div class="line">19</div><div class="line">20</div><div class="line">21</div><div class="line">22</div><div class="line">23</div><div class="line">24</div><div class="line">25</div><div class="line">26</div><div class="line">27</div><div class="line">28</div><div class="line">29</div><div class="line">30</div><div class="line">31</div><div class="line">32</div><div class="line">33</div><div class="line">34</div><div class="line">35</div><div class="line">36</div><div class="line">37</div><div class="line">38</div></pre></td><td class="code"><pre><div class="line">#取某几列</div><div class="line">awk '{print $2,$4,$5}' input.txt > output.txt</div><div class="line">cat *log|grep "variants loaded"|awk '{print $1}'|les</div><div class="line"></div><div class="line"># 查看文件有几列</div><div class="line">cat in.txt | awk '{print NF}'</div><div class="line"></div><div class="line"># -F 修改分隔符为冒号：</div><div class="line">awk -F: '{print $1}' in.txt</div><div class="line">awk -F" " '{print $1}' in.txt</div><div class="line"></div><div class="line"># 正则匹配、替换</div><div class="line">awk '/^test[0-9]+/' input.txt</div><div class="line">awk '$1 ~ /^test[0-9]+/' input.txt</div><div class="line">awk '{if($5==66) print $0}' input.txt</div><div class="line"></div><div class="line">sed 's/good/bad/' input.txt # 默认只替换第一个匹配</div><div class="line">sed 's/good/bad/2' input.txt # 只替换第二个匹配</div><div class="line">sed 's/good/bad/g' input.txt # 替换所有匹配</div><div class="line"></div><div class="line"># 三行程序，以“;”分割</div><div class="line">awk '{BASELINE=42; if($1>BASELINE) $5=$5+100; print $0}' data.f</div><div class="line"></div><div class="line"># 几列之间运算 calculate the sum of column 2 and 3 and put it at the end of a row or replace the first column:</div><div class="line">awk '{print $0,$2+$3}' input.txt</div><div class="line">awk '{$1=$2+$3;print}' input.txt</div><div class="line"></div><div class="line"># 取出文件某几行，比如5-10行</div><div class="line">sed -n '10p' data.txt # 打印第十行</div><div class="line">sed -n '5,10p' data.txt # 打印第5-10行</div><div class="line">sed -n '1-5p' data.txt # 打印第一行，跳过5行，打印第六行</div><div class="line">awk 'NR>=5&&NR<=10' data.txt</div><div class="line"></div><div class="line"># 文本、excel文件里面有空的项目不好split的时候，把空的用“-”填充</div><div class="line">less input.txt | sed ‘s/\t\t/\t\-\t/g;s/\t$/\t\-/g’ > output.txt</div><div class="line"></div><div class="line"># 输出一个tab分割的文件头</div><div class="line">echo "chr pos A1 A2 OR p-value"|awk -v OFS="\t" '{print $1,$2,$3,$4,$5,$6}'</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="ls长度限制问题-“-bin-ls-Argument-list-too-long”"><a href="#ls长度限制问题-“-bin-ls-Argument-list-too-long”" class="headerlink" title="ls长度限制问题 “/bin/ls: Argument list too long”"></a>ls长度限制问题 “/bin/ls: Argument list too long”</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line">find /DirName/ -name *.txt |less -N</div><div class="line">for i in DirName/*;do echo "ls $i " >> list.txt;done</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="rm-files-in-ls-grep"><a href="#rm-files-in-ls-grep" class="headerlink" title="rm files in ls/grep"></a>rm files in ls/grep</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">ls * | while read dd; do rm -rf $dd; done</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="tr"><a href="#tr" class="headerlink" title="tr"></a>tr</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line"># 把回车都替换成空格</div><div class="line">awk '{print $1}' in.txt|tr "\n" " "|less</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="纵向合并文件"><a href="#纵向合并文件" class="headerlink" title="纵向合并文件"></a>纵向合并文件</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">paste a.txt b.txt > ab.txt</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="wc"><a href="#wc" class="headerlink" title="wc"></a>wc</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div></pre></td><td class="code"><pre><div class="line">#显示文件内容信息,输出信息依次是:行数,字数,字节数,文件名称 </div><div class="line">wc filename </div><div class="line"></div><div class="line">#显示一个文件的行数 </div><div class="line">wc -l filename </div><div class="line"></div><div class="line">#显示一个文件的字节数 </div><div class="line">wc -c filename </div><div class="line"></div><div class="line">#显示一个文件的字符数 </div><div class="line">wc -m filename </div><div class="line"></div><div class="line">#显示一个文件中的最长行的长度 </div><div class="line">wc -L filename </div><div class="line"></div><div class="line">#注意：每行结尾的换行符也算一个字符，空格也算一个字符 </div><div class="line">#采用UTF-8编码，所以一个汉字在这里被转换为3字节 </div><div class="line">#当使用-m选项时，一个汉字就作为一个字符计算</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="find"><a href="#find" class="headerlink" title="find"></a>find</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line">find . -name ‘*.pl’</div><div class="line">find /path/dir -regextype "posix-egrep" -regex ".*\.(pl|sh|py|r|pdf|)$"</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="fasta-fastq-vcf"><a href="#fasta-fastq-vcf" class="headerlink" title="fasta/fastq/vcf"></a>fasta/fastq/vcf</h2><ul>
<li><p>取fasta中的某一段序列（代替perl里的substr效果）</p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">samtools faidx hg19.fasta chr1:1-100</div></pre></td></tr></table></figure>
</li>
<li><p>为vcf文件建索引，GATK依赖</p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line">samtools/htslib/bgzip -c file.vcf > file.vcf.gz</div><div class="line">samtools/htslib/tabix -p vcf file.vcf.gz</div></pre></td></tr></table></figure>
</li>
</ul>
<p><br></p>
<h2 id="Example-header-of-PBS-qsub-Command-Lines"><a href="#Example-header-of-PBS-qsub-Command-Lines" class="headerlink" title="Example header of PBS(qsub) Command Lines"></a>Example header of PBS(qsub) Command Lines</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div></pre></td><td class="code"><pre><div class="line">#$ -S /bin/sh</div><div class="line">#$ -e z.1.sh.SuperMem-1.pbs.$JOB_ID.e</div><div class="line">#$ -o z.1.sh.SuperMem-1.pbs.$JOB_ID.o</div><div class="line">#$ -l vf=1G</div><div class="line">#$ -m n</div><div class="line">#$ -cwd</div><div class="line">#$ -P st_supermem</div><div class="line">#$ -q supermem.q@supermem-0-2</div><div class="line"># 指定supermem-0-2节点</div><div class="line"></div><div class="line"># start time</div><div class="line">date1=`date "+%Y-%m-%d %H:%M:%S"`; date1_sys=`date -d "$date1" +%s`;echo "start running ========= at $date1"</div><div class="line"></div><div class="line">perl test.pl</div><div class="line"></div><div class="line"># end time and running time; output to z.1.sh.SuperMem-1.pbs.$JOB_ID.o</div><div class="line">date2=`date "+%Y-%m-%d %H:%M:%S"`; date2_sys=`date -d "$date2" +%s`; interval=`expr $date2_sys - $date1_sys`; hour=`expr $interval / 3600`;left_second=`expr $interval % 3600`; min=`expr $left_second / 60`; second=`expr $interval % 60`; echo "done running ========= at $date2 in $hour hour $min min $second s"</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="kill"><a href="#kill" class="headerlink" title="kill"></a>kill</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div></pre></td><td class="code"><pre><div class="line"># 一次杀掉所有进程，慎用</div><div class="line">pgrep -u wanglizhong |xargs kill</div><div class="line"></div><div class="line">kill -9 $(ps -ef|grep wanglizhong|awk '{print $2}')</div><div class="line"></div><div class="line">pkill -u wanglizhong</div><div class="line"></div><div class="line">skill -KILL -u username</div></pre></td></tr></table></figure>
<p><br></p>
<h2 id="解压-压缩"><a href="#解压-压缩" class="headerlink" title="解压/压缩"></a>解压/压缩</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div><div class="line">19</div><div class="line">20</div><div class="line">21</div><div class="line">22</div><div class="line">23</div><div class="line">24</div><div class="line">25</div><div class="line">26</div><div class="line">27</div><div class="line">28</div><div class="line">29</div><div class="line">30</div><div class="line">31</div><div class="line">32</div><div class="line">33</div><div class="line">34</div><div class="line">35</div><div class="line">36</div><div class="line">37</div><div class="line">38</div><div class="line">39</div><div class="line">40</div><div class="line">41</div><div class="line">42</div><div class="line">43</div><div class="line">44</div><div class="line">45</div><div class="line">46</div><div class="line">47</div><div class="line">48</div><div class="line">49</div><div class="line">50</div><div class="line">51</div><div class="line">52</div><div class="line">53</div><div class="line">54</div><div class="line">55</div><div class="line">56</div><div class="line">57</div><div class="line">58</div><div class="line">59</div><div class="line">60</div><div class="line">61</div><div class="line">62</div><div class="line">63</div><div class="line">64</div><div class="line">65</div><div class="line">66</div><div class="line">67</div><div class="line">68</div><div class="line">69</div><div class="line">70</div><div class="line">71</div><div class="line">72</div><div class="line">73</div><div class="line">74</div><div class="line">75</div><div class="line">76</div><div class="line">77</div><div class="line">78</div><div class="line">79</div><div class="line">80</div><div class="line">81</div><div class="line">82</div><div class="line">83</div><div class="line">84</div><div class="line">85</div><div class="line">86</div><div class="line">87</div><div class="line">88</div><div class="line">89</div><div class="line">90</div><div class="line">91</div><div class="line">92</div><div class="line">93</div><div class="line">94</div><div class="line">95</div></pre></td><td class="code"><pre><div class="line">.tar</div><div class="line">解包：tar xvf Something.tar</div><div class="line">打包：tar cvf Something.tar DirName</div><div class="line">（注：tar是打包，不是压缩！）</div><div class="line">———————————————</div><div class="line">.gz</div><div class="line">解压1：gunzip Something.gz</div><div class="line">解压2：gzip -d Something.gz</div><div class="line">压缩：gzip Something</div><div class="line"></div><div class="line">.tar.gz 和 .tgz</div><div class="line">解压：tar zxf Something.tar.gz</div><div class="line">压缩：tar zcf Something.tar.gz DirName</div><div class="line"></div><div class="line">分卷压缩tar.gz: tar zcf - DirName/* |split -d -b 100m - Something.tar.gz.</div><div class="line"># 生成文件：Something.tar.gz.00 Something.tar.gz.01 Something.tar.gz.02 ...</div><div class="line">解压tar.gz分卷</div><div class="line">cat Something.tar.gz.* | tar zx</div><div class="line">———————————————</div><div class="line">.bz2</div><div class="line">解压1：bzip2 -d Something.bz2</div><div class="line">解压2：bunzip2 Something.bz2</div><div class="line">压缩： bzip2 -z Something</div><div class="line"></div><div class="line">.tar.bz2</div><div class="line">解压：tar jxvf Something.tar.bz2</div><div class="line">压缩：tar jcvf Something.tar.bz2 DirName</div><div class="line"></div><div class="line">分卷压缩tar.bz2: tar jcf - DirName/* |split -d -b 100m - Something.tar.bz2.</div><div class="line"># 生成文件： Something.tar.bz2.00 Something.tar.bz2.01 Something.tar.bz2.02 ...</div><div class="line">解压tar.bz2分卷: cat logs.tar.gz* | tar jx</div><div class="line">———————————————</div><div class="line">.bz</div><div class="line">解压1：bzip2 -d Something.bz</div><div class="line">解压2：bunzip2 Something.bz</div><div class="line">压缩：未知</div><div class="line"></div><div class="line">.tar.bz</div><div class="line">解压：tar jxvf Something.tar.bz</div><div class="line">压缩：未知</div><div class="line">———————————————</div><div class="line">.Z</div><div class="line">解压：uncompress Something.Z</div><div class="line">压缩：compress Something</div><div class="line">.tar.Z</div><div class="line"></div><div class="line">解压：tar Zxvf Something.tar.Z</div><div class="line">压缩：tar Zcvf Something.tar.Z DirName</div><div class="line">———————————————</div><div class="line">.zip</div><div class="line">解压：unzip Something.zip</div><div class="line">压缩：zip Something.zip DirName/*</div><div class="line"></div><div class="line"># 大于2G的文件unzip可能有问题</div><div class="line">分卷：split Something.zip -b 100m -d Something2.zip</div><div class="line">分解解压：cat Something2.zip* > Something3.zip; unzip Something3.zip</div><div class="line">———————————————</div><div class="line">.rar</div><div class="line">解压：rar x Something.rar</div><div class="line">压缩：rar a Something.rar DirName</div><div class="line">———————————————</div><div class="line">.lha</div><div class="line">解压：lha -e Something.lha</div><div class="line">压缩：lha -a Something.lha Something</div><div class="line">———————————————</div><div class="line">.rpm</div><div class="line">解包：rpm2cpio Something.rpm | cpio -div</div><div class="line">#———————————————</div><div class="line">.deb</div><div class="line">解包：ar p Something.deb data.tar.gz | tar zxf -</div><div class="line">———————————————</div><div class="line">.tar .tgz .tar.gz .tar.Z .tar.bz .tar.bz2 .zip .cpio .rpm .deb .slp .arj .rar .ace .lha .lzh .lzx .lzs .arc .sda .sfx .lnx .zoo .cab .kar .cpt .pit .sit .sea</div><div class="line">解压：sEx x Something.*</div><div class="line">压缩：sEx a Something.* Something</div><div class="line"></div><div class="line">.tar.xz (xz http://tukaani.org/xz/)</div><div class="line">xz -d Something.tar.xz</div><div class="line"></div><div class="line"># gzip 压缩比</div><div class="line">-num 用指定的数字 num 调整压缩的速度，-1 或 --fast 表示最快压缩方法（低压缩比），-9 或--best表示最慢压缩方法（高压缩比）。系统缺省值为 6。</div><div class="line"></div><div class="line"></div><div class="line">.7z</div><div class="line"># download and install: https://sourceforge.net/projects/p7zip/files/p7zip/</div><div class="line">tar xjvf p7zip_9.20.1_x86_linux_bin.tar.bz2</div><div class="line">cd p7zip_9.20.1</div><div class="line">sh install.sh</div><div class="line"></div><div class="line">.7z</div><div class="line">解压：</div><div class="line">7za x file.7z -r -o./</div><div class="line">(-o后是没有空格的，直接接目录)</div><div class="line"></div><div class="line">压缩：</div><div class="line">7za a -t7z -r out.7z /dir/*</div></pre></td></tr></table></figure>
<h2 id="python-install-packages"><a href="#python-install-packages" class="headerlink" title="python install packages"></a>python install packages</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div></pre></td><td class="code"><pre><div class="line"># set PYTHONPATH</div><div class="line">export PYTHONPATH=/data/users/wlz/lib/python2.7/site-packages:/data/users/wlz:$PYTHONPATH</div><div class="line"></div><div class="line"># pip</div><div class="line">pip install --user pysnptools</div><div class="line">pip install --user matplotlib==1.4.3 #指定版本号</div><div class="line"></div><div class="line"># easy_install</div><div class="line">easy_install -d /data/users/wlz/lib/python2.7/site-packages pysnptools</div><div class="line"></div><div class="line"># download source code</div><div class="line">python setup.py install --prefix=/data/users/wlz</div></pre></td></tr></table></figure>
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<h2 id="信息检索"><a href="#信息检索" class="headerlink" title="信息检索"></a>信息检索</h2><p><a href="https://hk.lexiscn.com/" target="_blank" rel="external">法律，律商</a><br><a href="http://www.hibor.com.cn/" target="_blank" rel="external">金融，慧博</a><br><a href="http://www.cninfo.com.cn/" target="_blank" rel="external">公司财报,巨潮</a><br><a href="http://www.gsxt.gov.cn/" target="_blank" rel="external">查询公司信息，国家企业信用信息公示系统</a><br><a href="http://www.stats.gov.cn/" target="_blank" rel="external">国家统计局</a></p>
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卡方独立性检验chiq.test
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<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div><div class="line">19</div><div class="line">20</div><div class="line">21</div><div class="line">22</div><div class="line">23</div><div class="line">24</div><div class="line">25</div><div class="line">26</div><div class="line">27</div><div class="line">28</div><div class="line">29</div><div class="line">30</div><div class="line">31</div><div class="line">32</div></pre></td><td class="code"><pre><div class="line"># method 1</div><div class="line">> x=c(454,1833,2120)</div><div class="line">> y=c(52,216,240)</div><div class="line">> df=as.table(rbind(x,y))</div><div class="line"># df=as.table(rbind(c(454,1833,2120),c(52,216,240)))</div><div class="line"></div><div class="line">> df</div><div class="line">A B C</div><div class="line">A 454 1833 2120</div><div class="line">B 52 216 240</div><div class="line"></div><div class="line">> chisq.test(df)</div><div class="line">Pearson's Chi-squared test</div><div class="line"></div><div class="line">data: df</div><div class="line">X-squared = 0.1661, df = 2, p-value = 0.9203</div><div class="line"></div><div class="line"></div><div class="line"></div><div class="line"># method 2</div><div class="line">> df2=matrix(c(454,1833,2120,52,216,240),nr=3)</div><div class="line">> df2</div><div class="line">[,1] [,2]</div><div class="line">[1,] 454 52</div><div class="line">[2,] 1833 216</div><div class="line">[3,] 2120 240</div><div class="line"></div><div class="line">> chisq.test(df2)</div><div class="line">Pearson's Chi-squared test</div><div class="line"></div><div class="line">data: df2</div><div class="line">X-squared = 0.1661, df = 2, p-value = 0.9203</div></pre></td></tr></table></figure>
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Biomedical information search
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<h2 id="信息检索"><a href="#信息检索" class="headerlink" title="信息检索"></a>信息检索</h2><p>CN:<br><a href="https://dxy.com/" target="_blank" rel="external">丁香医生</a><br><a href="https://www.msdmanuals.com/zh/%E9%A6%96%E9%A1%B5" target="_blank" rel="external">默沙东诊疗手册-大众版</a><br><a href="https://www.msdmanuals.com/zh/%E4%B8%93%E4%B8%9A" target="_blank" rel="external">默沙东诊疗手册-专业版</a><br><a href="https://h5.baike.qq.com/mobile/home.html?adtag=ow&VNK=f6032155" target="_blank" rel="external">腾讯医典</a><br><a href="http://www.who.int/zh" target="_blank" rel="external">WHO世界卫生组织</a><br><a href="http://dg.cnsoc.org/index.html" target="_blank" rel="external">中国居民膳食指南</a><br><a href="http://www.a-hospital.com/w/%E9%A6%96%E9%A1%B5" target="_blank" rel="external">A+医学百科</a></p>
<p>EN:<br><a href="https://www.mayoclinic.org/" target="_blank" rel="external">梅奥诊所MayoClinic</a><br><a href="https://www.healthline.com/" target="_blank" rel="external">healthline</a><br><a href="https://ods.od.nih.gov/factsheets/list-all/" target="_blank" rel="external">NIH膳食营养说明</a><br><a href="https://www.webmd.com/a-to-z-guides/common-topics" target="_blank" rel="external">WebMd</a><br><a href="https://www.cdc.gov/" target="_blank" rel="external">美国CDC</a><br><a href="https://health.gov/our-work/food-nutrition/2015-2020-dietary-guidelines" target="_blank" rel="external">美国Dietary Guidelines 2015-2020</a><br><a href="https://ghr.nlm.nih.gov/" target="_blank" rel="external">NIH遗传相关的查询Genetics Home Reference</a></p>
<p>Gene:<br><a href="https://www.nlm.nih.gov/mesh/" target="_blank" rel="external">NCBI Mesh+PubMed</a><br><a href="https://www.genecards.org" target="_blank" rel="external">GeneCards</a><br><a href="http://www.wikigenes.org/" target="_blank" rel="external">WikiGene</a><br><a href="https://www.ncbi.nlm.nih.gov/books/NBK1116/" target="_blank" rel="external">GeneReviews</a></p>
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<a class="post-title-link" href="/2018/06/12/install-emacs/" itemprop="url">
install emacs
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<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div></pre></td><td class="code"><pre><div class="line">wget http://mirrors.ustc.edu.cn/gnu/emacs/emacs-26.1.tar.gz</div><div class="line">tar zxvf emacs-26.1.tar.gz</div><div class="line">cd emacs-26.1</div><div class="line">./configure --prefix=/home/wlz/software/emacs/emacs-26.1 --with-x-toolkit=no --with-xpm=no --with-gif=no --with-tiff=no --with-gnutls=no</div><div class="line">make</div><div class="line">make install</div></pre></td></tr></table></figure>
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<a class="post-title-link" href="/2018/03/05/各色DNA和WEGENE开箱比较/" itemprop="url">
各色DNA 和 WEGENE 开箱比较
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2018-03-05
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<p><img src="http://ofr9vioug.bkt.clouddn.com/基因占卜.png" alt="image"></p>
<p><strong>个人基因组</strong>（Personal Genomics）相关的话题持续火爆，从科研大牛 George church 的新公司 Nebula Genomics 打算用虚拟货币购买用户的基因组数据，到《MIT科技评论》评选的十大技术突破榜单中的 <strong>基因占卜（Genetic Fortune-Telling）</strong>。</p>
<p>不知道你是否体验过个人基因组有关的产品，我在2016年就体验了<strong>“中国版23andMe”的 微基因（WEGENE）</strong> 的个人基因组产品，WEGENE 也是国内比较早（2015）开始做个人基因组相关业务、同时活到今天仍然活的不错的公司。</p>
<p>WEGENE 之前和之后，也有出现其他各种提供个人基因组产品的公司，要么已经没有消息了、要么总感觉是简单粗暴的模仿，没有想体验的欲望。</p>
<p>前段时间刷微博的时候，通过 @河森堡 和 @女王C-cup 微博发的“过年胖几斤”研究，偶然发现了 各色DNA（各色科技），一个致力于解读用户”行为-基因组遗传数据“关联的个人基因组公司。各色DNA 是 大象工会 内部孵化出来的项目、有 @黄章晋ster 的背书、创始人郭婷婷是原中科院认知神经科学博士研究生；<strong>“各色” 源于对DNA的隐喻：DNA是一个人的底色，它和你一生发生的事情、你的成长环境共同组成了现在的你。</strong></p>
<p>加上最近集中看到好几篇 23andMe 根据用户自我报告数据（self-reported data）所做的精神类和行为类基因组关联分析（Genome-wide association study，GWAS）研究。感觉 各色 可能走在了正确的 B2China 道路上，买了一份体验了一下。</p>
<p>顺便和之前做过的 WEGENE 进行一个简单的开箱体验比较。</p>
<hr>
<p>首先，说明一下各自产品的购买时间:</p>
<ul>
<li>微基因 购于2016年1月底，算是比较早期的产品包装。</li>
<li>各色DNA 购于2018年2月底。</li>
</ul>
<p><br><br><br></p>
<h2 id="外观"><a href="#外观" class="headerlink" title="外观"></a>外观</h2><p><img src="http://ofr9vioug.bkt.clouddn.com/外壳1.png" alt="image"><br>(左 WEGENE，右 各色DNA，下类似)</p>
<p>正面slogan：</p>
<ul>
<li>WEGENE：解读基因的秘密，遇见未来的自己。</li>
<li>各色：破解DNA密码的神奇之旅，即将开始。</li>
</ul>
<p><br><br><br></p>
<p><img src="http://ofr9vioug.bkt.clouddn.com/内容物1.png" alt="image"></p>
<p>核心内容是 唾液DNA样本采集管 ，附带一些纸质说明。</p>
<ul>
<li>WEGENE 盒子正方形、比较小，可参照顺丰快递单，内部用小盒子填满整个盒子，同时可能有防震作用，整体比较有设计感。可能和创始人的工业设计背景的“基因”有关。创始人之一的郑强的简介：</li>
</ul>
<blockquote>
<p>郑强，Wecenter开源问答程序创始人，Billwang工业设计社区创始人，连续多次创业，有丰富的互联网社区运营经验和资源。曾担任深圳市微客互动有限公司CEO（微客互动是华大科技、华大研究院、华大医学等的IT供应商，旗下Wecenter程序同时服务国内多个医疗机构和健康咨询平台）。</p>
</blockquote>
<ul>
<li>各色 盒子很大，大概A4纸大小、6厘米厚，内部没有明显的结构、相对简单，显得有点空。</li>
</ul>
<p>设计上WEGENE感觉风格化比较明显，与官方网站、微信订阅号图文的风格一致，而且早在2016年就已经形成比较一体的解决方案、成熟度比较高；各色 可能产品打磨时间相对短，互联网产品思维、可用的版本就先上、不纠结，感觉相对粗糙、零散一点，功能性OK。</p>
<p><img src="http://ofr9vioug.bkt.clouddn.com/gese2.png" alt="image"><br>各色 内部的文字材料，WEGENE的当时忘记拍照了</p>
<p><br><br><br></p>
<h2 id="物流"><a href="#物流" class="headerlink" title="物流"></a>物流</h2><p>DNA采样如果什么时候能突破物理限制，不用快递的话，那才能叫体验。</p>
<p>WEGENE 和 各色DNA 都是顺丰来回包邮，应该算是个人基因组产品的基本配置了；寄回方面，WEGENE 额外的是，有一张已经填好的顺丰快递单，无需填收件地址，比较贴心。</p>
<p><img src="http://ofr9vioug.bkt.clouddn.com/kuaididan.png" alt="image"></p>
<p><br><br><br></p>
<h2 id="核心部件：唾液DNA样本采集管"><a href="#核心部件：唾液DNA样本采集管" class="headerlink" title="核心部件：唾液DNA样本采集管"></a>核心部件：唾液DNA样本采集管</h2><p><img src="http://ofr9vioug.bkt.clouddn.com/采集管1.png" alt="image"></p>
<ul>
<li><p>WEGENE 是 唾液收集器 和 DNA保存液 分开为两管的设计，收集器体积较大，印象里采样当天早晨吐了很久才吐够。WEGENE 采用的 加拿大DNA Genotek 的唾液DNA采集管，好像成本比较高。</p>
</li>
<li><p>各色 是 唾液收集器 和 DNA保存液管子 二合一的设计。我手贱，以为自己是老司机，没看说明就直接不小心拧开了，保存液直接留到管子里、不方便密封了，打乱了我的采样计划。本来是打算和当时 WEGENE 采样一样，在第二天早晨、经过一晚上积累、口腔里脱落细胞较多的时候采集唾液，这样DNA足够多、成功率比较高。怕DNA保存液挥发变质，决定不等到明天了、漱个口一小时后采样。感觉这个二合一设计挺精巧的，可以节省物料，但是不够防呆。同时 收集器 的体积比较小，加上 采样器 本身插进去的体积占用，一口就吐满了；为了多收集点DNA，把采样器管子取出来之后，我又多吐了一点口水进去；但是盖子是内部突起的，实际体积又小了一点，关上盖的时候又溅出来一点。</p>
</li>
</ul>
<p><br><br><br></p>
<h2 id="整体感觉"><a href="#整体感觉" class="headerlink" title="整体感觉"></a>整体感觉</h2><p>WEGENE 包装完成度较高、易用性较好、设计感比较强；各色 的相对糙一点，和产品发展时间短、不够成熟也有关系，不过都不影响使用。</p>
<p>这两家虽然都是面向个人消费者的公司，但定位稍有不同：</p>
<ul>
<li><p>WEGENE “致力于让中国人受益于知道和理解的自己的基因组数据”，更加想让用户探索自身的秘密，“遇见未来的自己”。感觉定位更”23andMe”、更“科研”一些，从官方网站上看，行事风格上也更加沉稳，对DNA样品采集质量、祖源分析、人类遗传学相关的分析比较严谨。</p>
</li>
<li><p>各色 则定义自己聚焦「行为-基因关联分析」消费级产品，和大象工会背景的“基因”有关，有一定的用户迁移基础、也比较会做消费者传播。比较期待这群站在认知神经科学和新媒体交叉路口的人能“玩”出什么样的东西出来。</p>
</li>
</ul>
<p><img src="http://ofr9vioug.bkt.clouddn.com/6.png" alt="image"></p>
<p><br><br><br></p>
<p>相似的地方在于，他们都在用自己的方式让用户更加了解自己：</p>
<ul>
<li><p>了解自己的遗传信息，知道自己的现状和未来的可能性。</p>
</li>
<li><p>知道自己从何而来，与不同地域、不同时空、不同个性特质的人群产生联系，寻找那个“something bigger than yourself”的存在。</p>
</li>
<li><p>让科学研究的成果更可得、更容易理解；同时对于大样本、大数据的收集能反过来推动科研的进展，让每一个人尽早受益。</p>
</li>
</ul>
<p>用户规模上，微基因 有先发优势，截至2018年1月底“<a href="https://36kr.com/p/5116542.html" target="_blank" rel="external">WEGENE完成B轮融资，用户数已过10万，预计在2018年底将超过40万</a>”；各色科技 也势头很猛，2017年10月媒体报道“<a href="http://cj.sina.com.cn/article/detail/2695676131/430865" target="_blank" rel="external">收获了超10万人的行为数据，各色搭建了目前国内最大的基因-行为数据库，这个数字每天都在良性增长中</a>”。很有默契的和“10万+”关系上了，发展都很迅猛。</p>
<p>目前各色的样品还在我手上、打算明天寄出，等寄回分析报告出来之后，可以继续比较一下两家的详细内容。</p>
<p>更多内容，请关注、并留言说说你的想法。</p>
<hr>
<p>另外，WEGENE 最近有邀请好友立减返现的活动。</p>
<p>标准检测好友立减50，返现我39；全基因组立减1000，返现100。<br>刚好有需要的可以扫码或者 <a href="https://www.wegene.com/shop/?_source=R_1107_7F1CD0" target="_blank" rel="external">点击连接</a> 了解一下。<br><img src="http://ofr9vioug.bkt.clouddn.com/IMG_4268.PNG?imageView/2/w/500" alt="image"></p>
<p>PS：不是广告，但我希望能接到广告。</p>
<p>产品都是自己付费购买，如果不小心起到了广告效果，麻烦帮我at一下 @各色人类研究中心 和 @微基因WeGene 的小伙伴，请给我疯狂地打赏哈哈哈哈哈哈 (ˊ● ω ●ˋ)</p>
<p><img src="http://ofr9vioug.bkt.clouddn.com/1-打赏-二维码.png?imageView/2/w/500" alt="image"><br><img src="http://ofr9vioug.bkt.clouddn.com/打赏2.jpeg?imageView/2/w/500" alt="image"><br><img src="http://ofr9vioug.bkt.clouddn.com/1-公众号-关注-二维码.png?imageView/2/w/500" alt="image"></p>
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Calculate IBD using beagle and germline
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<h2 id="beagle"><a href="#beagle" class="headerlink" title="beagle"></a>beagle</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line">export JAVAHOME=/ifshk4/BC_PUB/biosoft/PIPE_RD/Package/java/jre1.8.0_45;</div><div class="line">/ifshk4/BC_PUB/biosoft/PIPE_RD/Package/java/jre1.8.0_45/bin/java -jar /ifshk5/PC_HUMAN_EU/USER/wanglizhong/software/beagle/4.1/beagle.27Jul16.86a.jar ibd=true impute=false window=50000 overlap=20000 ibdlod=3 ibdtrim=1500 gt=$vcf out=$out/$chr</div></pre></td></tr></table></figure>
<h2 id="germline"><a href="#germline" class="headerlink" title="germline"></a>germline</h2><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div></pre></td><td class="code"><pre><div class="line">my $vcftools="/home/wanglizhong/software/vcftools/vcftools-build/bin/vcftools";</div><div class="line">my $germline="/home/wanglizhong/software/germline/germline-1-5-1/germline";</div><div class="line"></div><div class="line">my @vcf=<01.VCF/*vcf.gz>;</div><div class="line">open(O,"> $0.sh");</div><div class="line"></div><div class="line">foreach my $vcf(@vcf){</div><div class="line"> print O "$vcftools --gzvcf $vcf --plink --out $vcf; ";</div><div class="line"> print O "$germline -min_m 1 -bits 128 -err_hom 0 -err_het 4 < $vcf.run;\n";</div><div class="line"> open(O2,"> $vcf.run");</div><div class="line"> print O2 "1\n$vcf.map\n$vcf.ped\n$vcf.out\n";</div><div class="line"> close O2;</div><div class="line">}</div><div class="line">close O;</div></pre></td></tr></table></figure>
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