Shell脚本获得核酸反向互补序列

DNA作为生物的遗传物质，由2条互补的链按照A-T,C-G碱基配对方式形成双螺旋结构。在生物信息处理时，常常需要得到已知序列的反向互补序列（反向是由于学术界约定俗成序列方向为5端到3端，因此只互补配对得到的是3端到5端的配对序列，还需要再反向一次变成5端到3端），诸如Python和其他专门的小工具都可以实现，但是这里尝试用Shell来解决问题。

• 问题：
  获得fasta格式核酸序列的反向互补配对序列。fasta格式中，>开头的是序列名称，后面的多行为具体的核酸序列，例如：
  >gene_name1
  ATACTCGATATGATGTAGTGATGTAGTGAGA
  CAGTGTGTTGTGTTGTTGTGGGTGTG
  >gene_name2
  ATACTCGATATGATGTAGTGATGTAGTGAGA
  CAGTGGTGGGTGTG

  
  
  
  
  
  
  
  
  
  
  
  
  
  

• 思路
  为了解决这个问题，首先介绍Shell中2个与此相关的命令：逆转字符串命令rev和翻译字符串命令tr;
  其次是使用bash的数组将每个序列名称和序列对应起来，形成类似与key-value的关系。

  
  
  
  

逆转：rev

• rev是逆转每一行字符串顺序的命令
• 使用语法
  rev [file …]
  
  

当指定文件时（一个或多个），返回文件每一行字符串逆序输出结果，没有指定文件时，则从标准输入读取

# 从文件逆转 [Neptuneyut]$ cat test.txt aaaaaaaaaaaaaaaaaaagggggggggggggggggggg [Neptuneyut]$ rev test.txt test.txt ggggggggggggggggggggaaaaaaaaaaaaaaaaaaa ggggggggggggggggggggaaaaaaaaaaaaaaaaaaa # 从标准输入读取 [Neptuneyut]$ echo aaaaaaaaaaaaaaaaaaagggggggggggggggggggg|rev ggggggggggggggggggggaaaaaaaaaaaaaaaaaaa 

• 应用
  获取反向互补序列
  
  

翻译：tr

tr用于翻译、压缩和删除字符串

• 语法
  Usage: tr [OPTION]… SET1 [SET2]
  将集合1中的字符替换为集合2中的字符，可以是一一对应的关系，例如set1中2个不同字符对应set2中2个不同字符；也可以是set1中多个字符对应set2中同一个字符。

  
  
  
  

• 选项
  -c, -C, –complement use the complement of SET1
  -d, –delete delete characters in SET1, do not translate
  -s, –squeeze-repeats replace each input sequence of a repeated character
  that is listed in SET1 with a single occurrence
  of that character
  -t, –truncate-set1 first truncate SET1 to length of SET2，默认进行集合替换

  
  
  
  
  
  
  
  
  
  
  
  

# 将at都替换成A，注意这里与正则式不同，不是将at作为整体替换掉 [Neptuneyut]$ echo aatc|tr at A AAAc 

• 支持的集合

\NNN character with octal value NNN (1 to 3 octal digits) \\ backslash \a audible BEL \b backspace \f form feed \n new line \r return \t horizontal tab \v vertical tab CHAR1-CHAR2 all characters from CHAR1 to CHAR2 in ascending order [CHAR*] in SET2, copies of CHAR until length of SET1 [CHAR*REPEAT] REPEAT copies of CHAR, REPEAT octal if starting with 0 [:alnum:] all letters and digits [:alpha:] all letters [:blank:] all horizontal whitespace [:cntrl:] all control characters [:digit:] all digits [:graph:] all printable characters, not including space [:lower:] all lower case letters [:print:] all printable characters, including space [:punct:] all punctuation characters [:space:] all horizontal or vertical whitespace [:upper:] all upper case letters [:xdigit:] all hexadecimal digits [=CHAR=] all characters which are equivalent to CHAR 

例如：

# 将小写字母转换成大写字母 [Neptuneyut]$ echo aaattt0|tr a-z A-Z AAATTT0 # 或者 [Neptuneyut]$ echo aaattt0|tr [:lower:] [:upper:] AAATTT0 # -c 将不在set1的字符替换为set2 [Neptuneyut]$ echo aaattt-0?9|tr -c a-z0-9 "\t" aaattt 0 9 # -d 不接set2，则将set1中的字符删除 [Neptuneyut]$ echo aaattt-0?9|tr -d a ttt-0?9 # -s 压缩 # 不接set2,压缩set1中连续的字符为1个 [Neptuneyut]$ echo aaattt-0?9 |tr -s at at-0?9 #接set2z，则将连续的set1字符压缩为1个set2字符 [Neptuneyut]$ echo aaattt-0?9 |tr -s t B aaaB-0?9 [Neptuneyut]$ echo aaattt-0?9 |tr -s at AT AT-0?9 

反向互补序列

# 生成互补序列 [Neptuneyut]$ echo atttcttcantgatgct|tr a-z A-Z |tr ATCG TAGC TAAAGAAGTNACTACGA [Neptuneyut]$ echo atttcttcantgatgct|tr a-z A-Z |tr ATCG TAGC |rev AGCATCANTGAAGAAAT # 生成反向序列 

fasta序列反向互补脚本

ReversedComplementationSequence.sh

#!/usr/bin/env bash # Author:yutao # Date:Tue Oct 22 13:40:49 CST 2019 # Description # To get the reversed complementation nucleotide sequence # Point: # Using bash array to restore ID and Sequence respectively input_seq=$1 #input nucleotide sequence,fasta format ID=() #initialization ID array ID+=($(grep ">" $input_seq)) #save the ID in the array SEQ=() #initialization Sequence array # sed -n "/pattern1/,/pattern2/p" file |sed "/>/d" to get the seq between two pattern for((i=0;i<${#ID[@]};i++)) do next_index=$((i+1)) #curretn index and next index start=${ID[i]} #pattern1 end=${ID[next_index]} #pattern2 seq=$(sed -n "/${start}/,/${end}/p" ${ 
    input_seq}|sed "/>/d"|tr -d "\n") #refromate multi-seq to single seq SEQ+=(${seq}) done for((i=0;i<${#ID[@]};i++)) do echo ${ID[i]} echo ${SEQ[i]}|tr a-z A-Z|tr ATCG TAGC |rev #reversing and complementary sequence done