_posts/2012-03-30-converting-fastq-to-fasta-with-simple-tools.md

   1 ---
   2 date: '2012-03-30 01:39:39'
   3 layout: post
   4 slug: converting-fastq-to-fasta-with-simple-tools
   5 title: "Converting FASTQ to FASTA with simple tools"
   6 description: ""
   7 category: BioInformatics
   8 tags: [Biology, Galaxy_Original, Linux, Tips, Scripts]
   9 wordpress_id: '1150'
  10 ---
  11 {% include JB/setup %}
  12
  13 又一次遇到fq文件要跑BLAST来鉴定物种污染情况，不想输出fasta文件浪费盘阵空间，就上网查on-the-fly的方法。（当然是简单命令走管道的……）
  14
  15 Google指向了老地方：<br>
  16 http://stackoverflow.com/questions/1542306/converting-fastq-to-fasta-with-sed-awk
  17
  18 Converting FASTQ to FASTA with SED/AWK
  19
  20 I have a data in that always comes in block of four in the following format (called FASTQ):
  21
  22     @SRR018006.2016 GA2:6:1:20:650 length=36
  23     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN
  24     +SRR018006.2016 GA2:6:1:20:650 length=36
  25     !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!+!
  26     @SRR018006.19405469 GA2:6:100:1793:611 length=36
  27     ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
  28     +SRR018006.19405469 GA2:6:100:1793:611 length=36
  29     7);;).;);;/;*.2>/@@7;@77<..;)58)5/>/
  30
  31 Is there a simple sed/awk/bash way to convert them into this format (called FASTA):
  32
  33     >SRR018006.2016 GA2:6:1:20:650 length=36
  34     NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN
  35     >SRR018006.19405469 GA2:6:100:1793:611 length=36
  36     ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
  37
  38 In principle we want to extract the first two lines in each block-of-4 and replace `@` with `>`.
  39
  40 * * *
  41
  42 下面是答案，不过Galaxy没直接选被打勾的那个……<br>
  43 This is the fastest I've got, and I stuck it in my .bashrc file:
  44 <pre lang="bash">alias fq2fa="awk '{print \">\" substr(\$0,2);getline;print;getline;getline}'"</pre>
  45 即：
  46 <pre lang="bash">awk '{print ">" substr($0,2);getline;print;getline;getline}'</pre>
  47 It doesn't fail on the infrequent but not impossible quality lines that start with @... but does fail on wrapped FASTQ, if that's even legal (it exists though).
  48
  49 另外有两个功能比较多的相关程序：
  50
  51 <ul>
  52         <li><a href="http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_to_fasta_usage">fastq_to_fasta from FASTX-Toolkit (FASTQ/A short-reads pre-processing tools)</a></li>
  53         <li><a href="http://prinseq.sourceforge.net/">prinseq (Easy and rapid quality control and data preprocessing)</a></li>
  54 </ul>
  55
  56 目前Galaxy断网中，有网且有空时再去考据这两软件。
  57