将某一多行的fasta文件转换为单行的fasta文件

处理数据的时候经常遇到将多行fasta转换为单行，或者将很多行fasta串联起来合并为一行，下面是一些方法。

vi test.fa

>a
AAAA
>b
CCCC
GGGG
>c
AAAA
GGGGG
CCCCCC
TTTTTTTT

目的文件：
>123
AGCTAGCTAAAA
>456
AAAATTTTCCCCAAAATTTTCCCC

或者
>a
AAAACCCCGGGGAAAAGGGGGCCCCCCTTTTTTTT

1、将多行fasta转换为单行的，并保留原来的头

awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' test.fa

>a
AAAA
>b
CCCCGGGG
>c
AAAAGGGGGCCCCCCTTTTTTTTTTTTTTTT

ps ： /^>/ { print n $0; n = "" } : 读取第一行时，因为n暂时不存在，所以不会出现第一行为空的情况

ps printf和print的区别：
printf不换行 print换行

2、将多行fasta文件转为单行，只保留一个头

sed '1!{/^>/d;}' test.fa | awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }'

>a
AAAACCCCGGGGAAAAGGGGGCCCCCCTTTTTTTT

3、写成一个小脚本

vi single_fa.sh

#! /bin/sh
func() {
    echo "Usage:"
    echo "single_fa.sh [-m mode(many or only)] [-n header name (if -m=only)] [-i input_file] [-o output_file]"
    echo "MODE:"
    echo "many: keep all header"
    echo "only: keep single header"
    exit -1
}

while getopts :m:n:i:o: varname
do
   let optnum++
   case $varname in
   m)
      mode="$OPTARG" ;;
   n)
      name="$OPTARG" ;;
   i)
      input="$OPTARG" ;;
   o)
      output="$OPTARG" ;;
   ?) 
      func ;;
   esac
done

if [ $mode = "many" ];then
     awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }'  $input > $output
elif test  "$name" ; then
     sed '1!{/^>/d;}' $input | awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' |sed  "1i\>$name" > $output
else 
     sed '1!{/^>/d;}' $input | awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }'  > $output
fi

运行演示

sh single_fa.sh -m many -i test.fa -o output.fa

cat output.fa
>123
AGCTAGCTAAAA
>456
AAAATTTTCCCCAAAATTTTCCCC

sh single_fa.sh -m only -i test.fa -o output.fa

cat output.fa
>123
AGCTAGCTAAAAAAAATTTTCCCCAAAATTTTCCCC

sh single_fa.sh -m only -i test.fa -o output.fa -n hahaha

cat output.fa
>hahaha
AGCTAGCTAAAAAAAATTTTCCCCAAAATTTTCCCC

部分内容参考自
https://stackoverflow.com/questions/15857088/remove-line-breaks-in-a-fasta-file
https://unix.stackexchange.com/questions/193246/how-can-i-detect-that-not-enough-options-were-passed-with-getopts