Question

我在一个文件夹中有几千个文件。每个文件的内容如下所示。我在这个例子中的文件名是：AAB08704.1.fasta

   >gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta]
   MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTE
   VHGVIMSLPVPFPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILI
   PARIH

我想跳过第一行，然后将剩余的行合并为一行。我的所有文件都以＆＃34;＆gt;＆＃34;开头这是标题信息，以下行是我想要合并为一行的序列信息。

我试过

    sed -i '2,$s/\n//g' AAB08704.1.fasta

我甚至尝试使用以下方法将multiline fasta转换为单行fasta：

   awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < AAB08704.1.fasta

这些命令都没有达到我的预期。任何线索？

预期产出：

   >gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta]
   MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTEVHGVIMSLPVPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILIPARIH

cat -A AAB08704.1.fasta给出了这个：

  M-oM-;M-?>gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta]^M$
  MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTE^M$
  VHGVIMSLPVPFPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILI^M$

Answer 1

使用perl

$ perl -pe 's/\n// if $. > 1 && !eof' AAB08704.1.fasta 
>gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta]
MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTEVHGVIMSLPVPFPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILIPARIH

s/\n//删除换行符
- if $. > 1 && !eof仅当行号大于1而不是文件结尾
使用perl -i -pe进行就地编辑。有关-i，-p和-e

Command Switches

Answer 2

喜欢这个？对于GNU awk：

$ awk '{p=p $0 (FNR==1?ORS:"")}ENDFILE{print p;p=""}' file file
>gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta]
MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTEVHGVIMSLPVPFPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILIPARIH
>gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta]
MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTEVHGVIMSLPVPFPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILIPARIH

这个删除第一条记录上>之前的所有字符：

$ awk 'FNR==1{sub(/^[^>]*/,"");p=$0 ORS;next}{p=p $0}ENDFILE{print p;p=""}' file file
>gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta]
MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTEVHGVIMSLPVPFPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILIPARIH
>gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta]
MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTEVHGVIMSLPVPFPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILIPARIH

Answer 3

sed是面向行的，因此需要在缓冲区中加载行而不是删除\n

sed -i -e '1d' -e 'H;${x;s/\n//g}' AAB08704.1.fasta

awk可以在行为中进行调整

awk 'BEGIN{FS="\n";RS="()";OFS=""}{$1="";$0=$0 ""}' AAB08704.1.fasta > tmp && mv tmp AAB08704.1.fasta

# or 
awk '!a++{next}{printf( "%s", $0) > (FILENAME ".tmp")}' AAB08704.1.fasta && mv AAB08704.1.fasta.tmp AAB08704.1.fasta
# or
awk 'NR>1{printf("%s",$0)}' AAB08704.1.fasta > tmp && mv tmp AAB08704.1.fasta

Answer 4

这也有效：

awk 'BEGIN{ ORS = "" }/^>/{ print $0, "\n"}NR>1{ print $0 }' file

输出：

>gi|1117824|gb|AAB08704.1| ecdysteroid regulated 16 kDa [Manduca sexta] 
MLFYITVTVLLVSAQAKFYTDCGSKLATVQSVGVSGWPENARECVLKRNSNVTISIDFSPTTDVSAITTEVHGVIMSLPVPFPCRSPDACKDNGLTCPIKAGVVANYKTTLPVLKSYPKVSVDVKWELKKDEEDLVCILIPARIH

在跳过标题的文件中将多行合并为单行

4 个答案: